1
|
Sreenivasan S, Heffren P, Suh K, Rodnin MV, Kosa E, Fenton AW, Ladokhin AS, Smith PE, Fontes JD, Swint‐Kruse L. The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm? Protein Sci 2024; 33:e4863. [PMID: 38073129 PMCID: PMC10806935 DOI: 10.1002/pro.4863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
During protein evolution, some amino acid substitutions modulate protein function ("tuneability"). In most proteins, the tuneable range is wide and can be sampled by a set of protein variants that each contains multiple amino acid substitutions. In other proteins, the full tuneable range can be accessed by a set of variants that each contains a single substitution. Indeed, in some globular proteins, the full tuneable range can be accessed by the set of site-saturating substitutions at an individual "rheostat" position. However, in proteins with intrinsically disordered regions (IDRs), most functional studies-which would also detect tuneability-used multiple substitutions or small deletions. In disordered transcriptional activation domains (ADs), studies with multiple substitutions led to the "acidic exposure" model, which does not anticipate the existence of rheostat positions. In the few studies that did assess effects of single substitutions on AD function, results were mixed: the ADs of two full-length transcription factors did not show tuneability, whereas a fragment of a third AD was tuneable by single substitutions. In this study, we tested tuneability in the AD of full-length human class II transactivator (CIITA). Sequence analyses and experiments showed that CIITA's AD is an IDR. Functional assays of singly-substituted AD variants showed that CIITA's function was highly tuneable, with outcomes not predicted by the acidic exposure model. Four tested positions showed rheostat behavior for transcriptional activation. Thus, tuneability of different IDRs can vary widely. Future studies are needed to illuminate the biophysical features that govern whether an IDR is tuneable by single substitutions.
Collapse
Affiliation(s)
- Shwetha Sreenivasan
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Paul Heffren
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
- Present address:
Department of BiosciencesKansas City UniversityKansas CityMissouriUSA
| | - Kyung‐Shin Suh
- Department of ChemistryKansas State UniversityManhattanKansasUSA
| | - Mykola V. Rodnin
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Edina Kosa
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Aron W. Fenton
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Paul E. Smith
- Department of ChemistryKansas State UniversityManhattanKansasUSA
| | - Joseph D. Fontes
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Liskin Swint‐Kruse
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| |
Collapse
|
2
|
Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
| |
Collapse
|
3
|
Ladokhin AS. Track and Field of the Journal of Membrane Biology. J Membr Biol 2023; 256:299-300. [PMID: 37955796 DOI: 10.1007/s00232-023-00298-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
|
4
|
Rizzo S, Sikorski E, Park S, Im W, Vasquez‐Montes V, Ladokhin AS, Thévenin D. Promoting the activity of a receptor tyrosine phosphatase with a novel pH-responsive transmembrane agonist inhibits cancer-associated phenotypes. Protein Sci 2023; 32:e4742. [PMID: 37515426 PMCID: PMC10461461 DOI: 10.1002/pro.4742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 07/30/2023]
Abstract
Cell signaling by receptor protein tyrosine kinases (RTKs) is tightly controlled by the counterbalancing actions of receptor protein tyrosine phosphatases (RPTPs). Due to their role in attenuating the signal-initiating potency of RTKs, RPTPs have long been viewed as therapeutic targets. However, the development of activators of RPTPs has remained limited. We previously reported that the homodimerization of a representative member of the RPTP family (protein tyrosine phosphatase receptor J or PTPRJ) is regulated by specific transmembrane (TM) residues. Disrupting this interaction by single point mutations promotes PTPRJ access to its RTK substrates (e.g., EGFR and FLT3), reduces RTK's phosphorylation and downstream signaling, and ultimately antagonizes RTK-driven cell phenotypes. Here, we designed and tested a series of first-in-class pH-responsive TM peptide agonists of PTPRJ that are soluble in aqueous solution but insert as a helical TM domain in lipid membranes when the pH is lowered to match that of the acidic microenvironment of tumors. The most promising peptide reduced EGFR's phosphorylation and inhibited cancer cell EGFR-driven migration and proliferation, similar to the PTPRJ's TM point mutations. Developing tumor-selective and TM-targeting peptide binders of critical RPTPs could afford a potentially transformative approach to studying RPTP's selectivity mechanism without requiring less specific inhibitors and represent a novel class of therapeutics against RTK-driven cancers.
Collapse
Affiliation(s)
- Sophie Rizzo
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Eden Sikorski
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Soohyung Park
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Victor Vasquez‐Montes
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Damien Thévenin
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| |
Collapse
|
5
|
Rodnin MV, Vasques-Montes V, Kyrychenko A, Oliveira NFB, Kashipathy MM, Battaile KP, Douglas J, Lovell S, Machuqueiro M, Ladokhin AS. Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain. Toxins (Basel) 2023; 15:410. [PMID: 37505680 PMCID: PMC10467104 DOI: 10.3390/toxins15070410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023] Open
Abstract
Protonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pKa values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pKas ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pKa values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur.
Collapse
Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Victor Vasques-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Nuno F. B. Oliveira
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | | | - Justin Douglas
- COBRE Bio-NMR Laboratory, University of Kansas, Lawrence, KS 66045, USA;
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | - Miguel Machuqueiro
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| |
Collapse
|
6
|
Ladokhin AS. Ukrainian science in the context of its anticolonial struggle. BBA Adv 2023; 3:100093. [PMID: 37334276 PMCID: PMC10275747 DOI: 10.1016/j.bbadva.2023.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/30/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023] Open
Abstract
The current Special Issue entitled "Highlights of Ukrainian Molecular Biosciences" is dedicated to presenting recent contributions in the areas of biochemistry and biophysics, molecular biology and genetics, molecular and cellular physiology, and physical chemistry of biological macromolecules made by researchers either currently working in Ukraine or those who have obtained their training in Ukrainian institutions. Obviously, such a collection can present only a small sample of relevant studies, making the editorial task a particular challenge, as inevitably many deserving research groups were missed. In addition, we are greatly sorrowed that some of the invitees were unable to contribute due to the continued bombardments and military attacks perpetrated by Russia in Ukraine since 2014, and especially in 2022. This Introduction is also intended to provide a broader context for understanding of Ukraine's decolonization struggle, both in science and on the battlefield, and outlines suggestions for the global scientific community.
Collapse
|
7
|
Vasquez-Montes V, Goldberg AFX, Thévenin D, Ladokhin AS. Ca 2+ and Mg 2+ Influence the Thermodynamics of Peptide-Membrane Interactions. J Mol Biol 2022; 434:167826. [PMID: 36115657 PMCID: PMC10029193 DOI: 10.1016/j.jmb.2022.167826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 02/08/2023]
Abstract
Accurate quantitative estimates of protein-membrane interactions are critical to studies of membrane proteins. Here, we demonstrate that thermodynamic analyses based on current hydropathy scales do not account for the significant and experimentally determined effects that Ca2+ or Mg2+ have on protein-membrane interactions. We examined distinct modes of interaction (interfacial partitioning and folding and transmembrane insertion) by studying three highly divergent peptides: Bid-BH3 (derived from apoptotic regulator Bid), peripherin-2-derived prph2-CTER, and the cancer-targeting pH-Low-Insertion-Peptide (pHLIP). Fluorescence experiments demonstrate that adding 1-2 mM of divalent cations led to a substantially more favorable bilayer partitioning and insertion, with free energy differences of 5-15 kcal/mol.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Andrew F X Goldberg
- Eye Research Institute, Oakland University, Rochester, MI 48309, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, United States. https://twitter.com/TheveninLab
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, United States.
| |
Collapse
|
8
|
Vasquez‐Montes V, Tyagi V, Sikorski E, Kyrychenko A, Freites JA, Thévenin D, Tobias DJ, Ladokhin AS. Ca 2+ -dependent interactions between lipids and the tumor-targeting peptide pHLIP. Protein Sci 2022; 31:e4385. [PMID: 36040255 PMCID: PMC9366937 DOI: 10.1002/pro.4385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/31/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022]
Abstract
Cancerous tissues undergo extensive changes to their cellular environments that differentiate them from healthy tissues. These changes include changes in extracellular pH and Ca2+ concentrations, and the exposure of phosphatidylserine (PS) to the extracellular environment, which can modulate the interaction of peptides and proteins with the plasma membrane. Deciphering the molecular mechanisms of such interactions is critical for advancing the knowledge-based design of cancer-targeting molecular tools, such as pH-low insertion peptide (pHLIP). Here, we explore the effects of PS, Ca2+ , and peptide protonation state on the interactions of pHLIP with lipid membranes. Cellular studies demonstrate that exposed PS on the plasma membrane promotes pHLIP targeting. The magnitude of this effect is dependent on extracellular Ca2+ concentration, indicating that divalent cations play an important role in pHLIP targeting in vivo. The targeting mechanism is further explored with a combination of fluorescence and circular dichroism experiments in model membranes and microsecond-timescale all-atom molecular dynamics simulations. Our results demonstrate that Ca2+ is engaged in coupling peptide-lipid interactions in the unprotonated transmembrane conformation of pHLIP. The simulations reveal that while the pH-induced insertion leads to a strong depletion of PS around pHLIP, the Ca2+ -induced insertion has the opposite effect. Thus, extracellular levels of Ca2+ are crucial to linking cellular changes in membrane lipid composition with the selective targeting and insertion of pHLIP. The characterized Ca2+ -dependent coupling between pHLIP sidechains and PS provides atomistic insights into the general mechanism for lipid-coupled regulation of protein-membrane insertion by divalent cations.
Collapse
Affiliation(s)
- Victor Vasquez‐Montes
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Vivek Tyagi
- Department of ChemistryUniversity of CaliforniaIrvineCaliforniaUSA
| | - Eden Sikorski
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National UniversityKharkivUkraine
| | | | - Damien Thévenin
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | | | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| |
Collapse
|
9
|
Vasquez Montes V, Rodnin MV, Ladokhin AS. Lipids and divalent cations regulate BH3-independent activation of BAX and Bcl-xL. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
10
|
Kyrychenko A, Vasquez-Montes V, Ladokhin AS. Advantages of Quantitative Analysis of Depth-Dependent Fluorescence Quenching: Case Study of BAX. J Membr Biol 2022; 255:461-468. [PMID: 34994819 DOI: 10.1007/s00232-021-00211-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Abstract
Dynamic disorder of the lipid bilayer presents a challenge for establishing structure-function relationships in membrane proteins, especially to those that insert by refolding from soluble states, e.g., bacterial toxins and Bcl-2 apoptotic regulators. Because many high-resolution structural techniques cannot be easily applied to such systems, methods like depth-dependent fluorescence quenching gained prominence. Over three decades ago, Prof. Erwin London and his co-workers revolutionized the studies of membrane protein insertion by introducing a quantitative approach to the analysis of membrane quenching data and inspired many researchers to continue this work. Here, we illustrate how the application of the quantitative analysis yields new insights into previously published results. We have used the method of distribution analysis (DA) to calculate the precise immersion depth of NBD fluorophores selectively attached to various single-cysteine mutants of the apoptotic factor BAX from quenching data obtained with a series of spin-labeled lipids. The original qualitative analysis interpreted the higher quenching determined for shallower probes in positions flanking the helix 9 of BAX as evidence of a transmembrane helix 9 topology. The quantitative DA, however, revealed that a transmembrane topology of helix 9 of BAX is unlikely, as it would require labeling sites that are only 15 residues apart in a helical conformation to be separated by a transverse distance of over 45 Å.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160-7421, USA.
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv, 61022, Ukraine.
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160-7421, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160-7421, USA
| |
Collapse
|
11
|
O'Neil PT, Vasquez-Montes V, Swint-Kruse L, Baldwin MR, Ladokhin AS. Spectroscopic evidence of tetanus toxin translocation domain bilayer-induced refolding and insertion. Biophys J 2021; 120:4763-4776. [PMID: 34555358 PMCID: PMC8595737 DOI: 10.1016/j.bpj.2021.09.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022] Open
Abstract
Tetanus neurotoxin (TeNT) is an A-B toxin with three functional domains: endopeptidase, translocation (HCT), and receptor binding. Endosomal acidification triggers HCT to interact with and insert into the membrane, translocating the endopeptidase across the bilayer. Although the function of HCT is well defined, the mechanism by which it accomplishes this task is unknown. To gain insight into the HCT membrane interaction on both local and global scales, we utilized an isolated, beltless HCT variant (bHCT), which retained the ability to release potassium ions from vesicles. To examine which bHCT residues interact with the membrane, we widely sampled the surface of bHCT using 47 single-cysteine variants labeled with the environmentally sensitive fluorophore NBD. At neutral pH, no interaction was observed for any variant. In contrast, all NBD-labeled positions reported environmental change in the presence of acidic pH and membranes containing anionic lipids. We then examined the conformation of inserted bHCT using circular dichroism and intrinsic fluorescence. Upon entering the membrane, bHCT retained predominantly α-helical secondary structure, whereas the tertiary structure exhibited substantial refolding. The use of lipid-attached quenchers revealed that at least one of the three tryptophan residues penetrated deep into the hydrocarbon core of the membrane, suggesting formation of a bHCT transmembrane conformation. The possible conformational topology was further explored with the hydropathy analysis webtool MPEx, which identified a large, potential α-helical transmembrane region. Altogether, the spectroscopic evidence supports a model in which, upon acidification, the majority of TeNT bHCT entered the membrane with a concurrent change in tertiary structure.
Collapse
Affiliation(s)
- Pierce T O'Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Michael R Baldwin
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas.
| |
Collapse
|
12
|
Vasquez-Montes V, Ladokhin AS. Expanding MPEx Hydropathy Analysis to Account for Electrostatic Contributions to Protein Interactions with Anionic Membranes. J Membr Biol 2021; 254:109-117. [PMID: 33564913 DOI: 10.1007/s00232-021-00170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Hydropathy plots are a crucial tool to guide experimental design, as they generate predictions of protein-membrane interactions and their bilayer topology. The predictions are based on experimentally determined hydrophobicity scales, which provide an estimate for the propensity and stability of these interactions. A significant improvement to the accuracy of hydropathy analyses was provided by the development of the popular Wimley-White interfacial and octanol hydrophobicity scales. These scales have been previously incorporated into the freely available MPEx (Membrane Protein Explorer) online application. Here, we introduce a substantial update to MPEx that allows for the consideration of electrostatic contributions to the bilayer partitioning free energy. This component originates from the Coulombic attraction or repulsion of charges between proteins and membranes. Its inclusion in hydropathy calculations increases the accuracy of hydropathy plot predictions and extends their use to more complex systems (i.e., anionic membranes). We illustrate the application of this analysis to studies on the membrane selectivity of antimicrobial peptides, the membrane partitioning of ion-channel gating modifiers, and the amyloid proteins α-synuclein and Tau, as well as pH-dependent bilayer interactions of diphtheria toxin and apoptotic inhibitor Bcl-xL.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
13
|
Ladokhin AS, Kyrychenko A, Rodnin MV, Vasquez-Montes V. Conformational switching, refolding and membrane insertion of the diphtheria toxin translocation domain. Methods Enzymol 2021; 649:341-370. [PMID: 33712192 DOI: 10.1016/bs.mie.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Diphtheria toxin is among many bacterial toxins that utilize the endosomal pathway of cellular entry, which is ensured by the bridging of the endosomal membrane by the toxin's translocation (T) domain. Endosomal acidification triggers a series of conformational changes of the T-domain, that take place first in aqueous and subsequently in membranous milieu. These rearrangements ultimately result in establishing membrane-inserted conformation(s) and translocation of the catalytic moiety of the toxin into the cytoplasm. We discuss here the strategy for combining site-selective labeling with various spectroscopic methods to characterize structural and thermodynamic aspects of protonation-dependent conformational switching and membrane insertion of the diphtheria toxin T-domain. Among the discussed methods are FRET, FCS and depth-dependent fluorescence quenching with lipid-attached bromine atoms and spin probes. The membrane-insertion pathway of the T-domain contains multiple intermediates and is governed by staggered pH-dependent transitions involving protonation of histidines and acidic residues. Presented data demonstrate that the lipid bilayer plays an active part in T-domain functioning and that the so-called Open-Channel State does not constitute the translocation pathway, but is likely to be a byproduct of the translocation. The spectroscopic approaches presented here are broadly applicable to many other systems of physiological and biomedical interest for which conformational changes can lead to membrane insertion (e.g., other bacterial toxins, host defense peptides, tumor-targeting pHLIP peptides and members of Bcl-2 family of apoptotic regulators).
Collapse
Affiliation(s)
- Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS, United States.
| | - Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS, United States
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS, United States
| |
Collapse
|
14
|
Rodnin MV, Kashipathy MM, Kyrychenko A, Battaile KP, Lovell S, Ladokhin AS. Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain. Toxins (Basel) 2020; 12:toxins12110704. [PMID: 33171806 PMCID: PMC7695028 DOI: 10.3390/toxins12110704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 12/28/2022] Open
Abstract
Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5–6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2–3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.
Collapse
Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
| | - Maithri M. Kashipathy
- Protein Structure Laboratory, Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA; (M.M.K.); (S.L.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Kevin P. Battaile
- NYX beamline, New York Structural Biology Center, Upton, NY 11973, USA;
| | - Scott Lovell
- Protein Structure Laboratory, Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA; (M.M.K.); (S.L.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA; (M.V.R.); (A.K.)
- Correspondence: ; Tel.: +1-913-588-0489; Fax: +1-913-588-7440
| |
Collapse
|
15
|
Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol 2020; 253:287-298. [PMID: 32500172 DOI: 10.1007/s00232-020-00124-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/23/2020] [Indexed: 12/16/2022]
Abstract
Protegrin-1 (PG-1), an 18-residue β-hairpin stabilized by two disulfide bonds, is a member of a family of powerful antimicrobial peptides which are believed to act through membrane permeabilization. Here we used a combination of experimental and computational approaches to characterize possible structural arrangements of PG-1 in lipid bilayers mimicking bacterial membranes. We have measured the dose-response function of the PG-1-induced leakage of markers of various sizes from vesicles and found it to be consistent with the formation of pores of two different sizes. The first one allows the release of small dyes and occurs at peptide:lipid ratios < 0.006. Above this ratio, larger pores are observed through which the smallest of dextrans FD4 can be released. In parallel with pore formation, we observe a general large-scale destabilization of vesicles which is probably related to complete rupture of some vesicles. The population of vesicles that are completely ruptured depends linearly on PG-1:lipid ratio. Neither pore size, nor vesicle rupture are influenced by the formation of disulfide bonds. Previous computational work on oxidized protegrin is complemented here by all-atom MD simulations of PG-1 with reduced disulfide bonds both in solution (monomer) and in a bilayer (dimer and octamer). The simulations provide molecular insights into the influence of disulfide bonds on peptide conformation, aggregation, and oligomeric structure.
Collapse
Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Binod Nepal
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Themis Lazaridis
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, NY, 10016, USA.
| |
Collapse
|
16
|
Ladokhin AS. The Journal of Membrane Biology in 2020. J Membr Biol 2020; 253:79. [PMID: 32219485 DOI: 10.1007/s00232-020-00116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160-7421, USA.
| |
Collapse
|
17
|
Kyrychenko OV, Ladokhin AS. Accurate Determination of Membrane Penetration of Proteins Using Fluorescence Quenching and Molecular Dynamics Simulations. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
18
|
Vasquez-Montes V, Gerhart J, Thévenin D, Ladokhin AS. Divalent Cations and Lipid Composition Modulate Membrane Insertion and Cancer-Targeting Action of pHLIP. J Mol Biol 2019; 431:5004-5018. [PMID: 31689432 DOI: 10.1016/j.jmb.2019.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023]
Abstract
The pH-Low Insertion Peptide (pHLIP) has emerged as an important tool for targeting cancer cells; it has been assumed that its targeting mechanism depends solely on the mild acidic environment surrounding tumors. Here, we examine the role of Ca2+ and Mg2+ on pHLIP's insertion, cellular targeting, and drug delivery. We demonstrate that physiologically relevant concentrations of either cation can shift the protonation-dependent transition by up to several pH units toward basic pH and induce substantial protonation-independent transmembrane insertion of pHLIP at pH as high as 10. Consistent with these results, the ability of pHLIP to deliver the cytotoxic compound monomethyl-auristatin-F to HeLa cells is increased several fold in presence of Ca2+. Complementary measurements with model membranes confirmed this Ca2+/Mg2+-dependent membrane-insertion mechanism. The magnitude of this alternative Ca2+/Mg2+-dependent effect is also modulated by lipid composition-specifically by the presence of phosphatidylserine-providing new clues to pHLIP's unique tumor-targeting ability in vivo. These results exemplify the complex coupling between protonation of anionic residues and lipid-selective targeting by divalent cations, which is relevant to the general signaling on membrane interfaces.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA, 18015, USA
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA, 18015, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
19
|
Vasquez-Montes V, Vargas-Uribe M, Pandey NK, Rodnin MV, Langen R, Ladokhin AS. Lipid-modulation of membrane insertion and refolding of the apoptotic inhibitor Bcl-xL. Biochim Biophys Acta Proteins Proteom 2019; 1867:691-700. [PMID: 31004798 DOI: 10.1016/j.bbapap.2019.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Bcl-xL is a member of the Bcl-2 family of apoptotic regulators, responsible for inhibiting the permeabilization of the mitochondrial outer membrane, and a promising anti-cancer target. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (a) a soluble folded conformation, (b) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (c) refolded membrane-inserted conformations, for which no structural data are available. Previous studies established that in the cell Bcl-xL exists in a dynamic equilibrium between soluble and membranous states, however, no direct evidence exists in support of either anchored or inserted conformation of the membranous state in vivo. In this in vitro study, we employed a combination of fluorescence and EPR spectroscopy to characterize structural features of the bilayer-inserted conformation of Bcl-xL and the lipid modulation of its membrane insertion transition. Our results indicate that the core hydrophobic helix α6 inserts into the bilayer without adopting a transmembrane orientation. This insertion disrupts the packing of Bcl-xL and releases the regulatory N-terminal BH4 domain (α1) from the rest of the protein structure. Our data demonstrate that both insertion and refolding of Bcl-xL are modulated by lipid composition, which brings the apparent pKa of insertion to the threshold of physiological pH. We hypothesize that conformational rearrangements associated with the bilayer insertion of Bcl-xL result in its switching to a so-called non-canonical mode of apoptotic inhibition. Presented results suggest that the alteration in lipid composition before and during apoptosis can serve as an additional factor regulating the permeabilization of the mitochondrial outer membrane.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nitin K Pandey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| |
Collapse
|
20
|
Vasquez-Montes V, Rodnin MV, Ladokhin AS. Lipid-Dependent Modulation of Conformational Switching by Protonation during Membrane Protein Insertion. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
21
|
Rodnin MV, Vargas-Uribe M, Ladokhin AS. Cellular Entry of Diphtheria Toxin Does Not Require Formation of the Open-Channel State by its Translocation Domain. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
22
|
Affiliation(s)
- Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| |
Collapse
|
23
|
Vasquez-Montes V, Gerhart J, King KE, Thévenin D, Ladokhin AS. Comparison of lipid-dependent bilayer insertion of pHLIP and its P20G variant. Biochim Biophys Acta Biomembr 2017; 1860:534-543. [PMID: 29138065 DOI: 10.1016/j.bbamem.2017.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/18/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023]
Abstract
The ability of the pH-Low Insertion Peptide (pHLIP) to insert into lipid membranes in a transbilayer conformation makes it an important tool for targeting acidic diseased tissues. pHLIP can also serve as a model template for thermodynamic studies of membrane insertion. We use intrinsic fluorescence and circular dichroism spectroscopy to examine the effect of replacing pHLIP's central proline on the pH-triggered lipid-dependent conformational switching of the peptide. We find that the P20G variant (pHLIP-P20G) has a higher helical propensity than the native pHLIP (pHLIP-WT), in both water:organic solvent mixtures and in the presence of lipid bilayers. Spectral shifts of tryptophan fluorescence reveal that with both pHLIP-WT and pHLIP-P20G, the deeply penetrating interfacial form (traditionally called State II) is populated only in pure phosphocholine bilayers. The presence of either anionic lipids or phosphatidylethanolamine leads to a much shallower penetration of the peptide (referred to here as State IIS, for "shallow"). This novel state can be differentiated from soluble state by a reduction in accessibility of tryptophans to acrylamide and by FRET to vesicles doped with Dansyl-PE, but not by a spectral shift in fluorescence emission. FRET experiments indicate free energies for interfacial partitioning range from 6.2 to 6.8kcal/mol and are marginally more favorable for pHLIP-P20G. The effective pKa for the insertion of both peptides depends on the lipid composition, but is always higher for pHLIP-P20G than for pHLIP-WT by approximately one pH unit, which corresponds to a difference of 1.3kcal/mol in free energy of protonation favoring insertion of pHLIP-P20G.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Kelly E King
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States.
| |
Collapse
|
24
|
Rodnin MV, Li J, Gross ML, Ladokhin AS. The pH-Dependent Trigger in Diphtheria Toxin T Domain Comes with a Safety Latch. Biophys J 2017; 111:1946-1953. [PMID: 27806276 DOI: 10.1016/j.bpj.2016.09.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 01/01/2023] Open
Abstract
Protein-side-chain protonation, coupled to conformational rearrangements, is one way of regulating physiological function caused by changes in protein environment. Specifically, protonation of histidine residues has been implicated in pH-dependent conformational switching in several systems, including the diphtheria toxin translocation (T) domain, which is responsible for the toxin's cellular entry via the endosomal pathway. Our previous studies a) identified protonation of H257 as a major component of the T domain's conformational switch and b) suggested the possibility of a neighboring H223 acting as a modulator, affecting the protonation of H257 and preventing premature conformational changes outside the endosome. To verify this "safety-latch" hypothesis, we report here the pH-dependent folding and membrane interactions of the T domain of the wild-type and that of the H223Q mutant, which lacks the latch. Thermal unfolding of the T domain, measured by circular dichroism, revealed that the reduction in the transition temperature for helical unfolding for an H223Q mutant starts at less acidic conditions (pH <7.5) relative to the wild-type protein (pH <6.5). Hydrogen-deuterium-exchange mass spectrometry demonstrates that the H223Q replacement results in a loss of stability of the amphipathic helices TH1-3 and the hydrophobic core helix TH8 at pH 6.5. That this destabilization occurs in solution correlates well with the pH-range shift for the onset of the membrane permeabilization and translocation activity of the T domain, confirming our initial hypothesis that H223 protonation guards against early refolding. Taken together, these results demonstrate that histidine protonation can fine-tune pH-dependent switching in physiologically relevant systems.
Collapse
Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Jing Li
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas.
| |
Collapse
|
25
|
Kyrychenko A, Rodnin MV, Ghatak C, Ladokhin AS. Computational refinement of spectroscopic FRET measurements. Data Brief 2017; 12:213-221. [PMID: 28459092 PMCID: PMC5397103 DOI: 10.1016/j.dib.2017.03.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 01/02/2023] Open
Abstract
This article supplies raw data related to a research article entitled “Joint refinement of FRET measurements using spectroscopic and computational tools” (Kyrychenko et al., 2017) [1], in which we demonstrate the use of molecular dynamics simulations to estimate FRET orientational factors in a benchmark donor-linker-acceptor system of enhanced cyan (ECFP) and enhanced yellow (EYFP) fluorescent proteins. This can improve the recalculation of donor-acceptor distance information from single-molecule FRET measurements.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine.,Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Chiranjib Ghatak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center Kansas City, KS66160-7421, USA
| |
Collapse
|
26
|
Milstein ML, Kimler VA, Ghatak C, Ladokhin AS, Goldberg AFX. An inducible amphipathic helix within the intrinsically disordered C terminus can participate in membrane curvature generation by peripherin-2/rds. J Biol Chem 2017; 292:7850-7865. [PMID: 28325841 DOI: 10.1074/jbc.m116.768143] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/15/2017] [Indexed: 01/28/2023] Open
Abstract
Peripherin-2/rds is required for biogenesis of vertebrate photoreceptor outer segment organelles. Its localization at the high-curvature rim domains of outer segment disk membranes suggests that it may act to shape these structures; however, the molecular function of this protein is not yet resolved. Here, we apply biochemical, biophysical, and imaging techniques to elucidate the role(s) played by the protein's intrinsically disordered C-terminal domain and an incipient amphipathic α-helix contained within it. We investigated a deletion mutant lacking only this α-helix in stable cell lines and Xenopus laevis photoreceptors. We also studied a soluble form of the full-length ∼7-kDa cytoplasmic C terminus in cultured cells and purified from Escherichia coli The α-helical motif was not required for protein biosynthesis, tetrameric subunit assembly, tetramer polymerization, localization at disk rims, interaction with GARP2, or the generation of membrane curvature. Interestingly, however, loss of the helical motif up-regulated membrane curvature generation in cellulo, introducing the possibility that it may regulate this activity in photoreceptors. Furthermore, the incipient α-helix (within the purified soluble C terminus) partitioned into membranes only when its acidic residues were neutralized by protonation. This suggests that within the context of full-length peripherin-2/rds, partitioning would most likely occur at a bilayer interfacial region, potentially adjacent to the protein's transmembrane domains. In sum, this study significantly strengthens the evidence that peripherin-2/rds functions directly to shape the high-curvature rim domains of the outer segment disk and suggests that the protein's C terminus may modulate membrane curvature-generating activity present in other protein domains.
Collapse
Affiliation(s)
- Michelle L Milstein
- From the Eye Research Institute, Oakland University, Rochester, Michigan 48309 and
| | - Victoria A Kimler
- From the Eye Research Institute, Oakland University, Rochester, Michigan 48309 and
| | - Chiranjib Ghatak
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160-7421
| | - Alexey S Ladokhin
- the Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160-7421
| | - Andrew F X Goldberg
- From the Eye Research Institute, Oakland University, Rochester, Michigan 48309 and
| |
Collapse
|
27
|
Vasquez-Montes V, Burns KE, Thevenin D, Ladokhin AS. Lipid Headgroups Modulate Conformational Switching during Membrane Insertion of Cancer-Targeting pHLIP Peptides. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
28
|
Kyrychenko A, Rodnin MV, Ghatak C, Ladokhin AS. Joint refinement of FRET measurements using spectroscopic and computational tools. Anal Biochem 2017; 522:1-9. [PMID: 28108168 DOI: 10.1016/j.ab.2017.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/28/2022]
Abstract
The variability of the orientation factor is a long-standing challenge in converting FRET efficiency measurements into donor-acceptor distances. We propose the use of molecular dynamics (MD) simulations to characterize orientation distributions and thus improve the accuracy of distance measurements. Here, we test this approach by comparing experimental and simulated FRET efficiencies for a model donor-acceptor pair of enhanced cyan and enhanced yellow FPs connected by a flexible linker. Several spectroscopic techniques were used to characterize FRET in solution. In addition, a series of atomistic MD simulations of a total length of 1.5 μs were carried out to calculate the distances and the orientation factor in the FRET-pair. The resulting MD-based and experimentally measured FRET efficiency histograms coincided with each other, allowing for direct comparison of distance distributions. Despite the fact that the calculated average orientation factor was close to 2/3, the application of the average κ2 to the entire histogram of FRET efficiencies resulted in a substantial artificial broadening of the calculated distribution of apparent donor-acceptor distances. By combining single pair-FRET measurements with computational tools, we demonstrate that accounting for the donor and acceptor orientation heterogeneity is critical for accurate representation of the donor-acceptor distance distribution from FRET measurements.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.
| | - Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA
| | - Chiranjib Ghatak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.
| |
Collapse
|
29
|
Gnanasambandam R, Ghatak C, Yasmann A, Nishizawa K, Sachs F, Ladokhin AS, Sukharev SI, Suchyna TM. GsMTx4: Mechanism of Inhibiting Mechanosensitive Ion Channels. Biophys J 2017; 112:31-45. [PMID: 28076814 PMCID: PMC5231890 DOI: 10.1016/j.bpj.2016.11.013] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/12/2016] [Accepted: 11/03/2016] [Indexed: 12/21/2022] Open
Abstract
GsMTx4 is a spider venom peptide that inhibits cationic mechanosensitive channels (MSCs). It has six lysine residues that have been proposed to affect membrane binding. We synthesized six analogs with single lysine-to-glutamate substitutions and tested them against Piezo1 channels in outside-out patches and independently measured lipid binding. Four analogs had ∼20% lower efficacy than the wild-type (WT) peptide. The equilibrium constants calculated from the rates of inhibition and washout did not correlate with the changes in inhibition. The lipid association strength of the WT GsMTx4 and the analogs was determined by tryptophan autofluorescence quenching and isothermal calorimetry with membrane vesicles and showed no significant differences in binding energy. Tryptophan fluorescence-quenching assays showed that both WT and analog peptides bound superficially near the lipid-water interface, although analogs penetrated deeper. Peptide-lipid association, as a function of lipid surface pressure, was investigated in Langmuir monolayers. The peptides occupied a large fraction of the expanded monolayer area, but that fraction was reduced by peptide expulsion as the pressure approached the monolayer-bilayer equivalence pressure. Analogs with compromised efficacy had pressure-area isotherms with steeper slopes in this region, suggesting tighter peptide association. The pressure-dependent redistribution of peptide between "deep" and "shallow" binding modes was supported by molecular dynamics (MD) simulations of the peptide-monolayer system under different area constraints. These data suggest a model placing GsMTx4 at the membrane surface, where it is stabilized by the lysines, and occupying a small fraction of the surface area in unstressed membranes. When applied tension reduces lateral pressure in the lipids, the peptides penetrate deeper acting as "area reservoirs" leading to partial relaxation of the outer monolayer, thereby reducing the effective magnitude of stimulus acting on the MSC gate.
Collapse
Affiliation(s)
| | - Chiranjib Ghatak
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Anthony Yasmann
- Department of Biology, University of Maryland, College Park, Maryland
| | - Kazuhisa Nishizawa
- Clinical Laboratory Science, Teikyo University School of Medical Technology, Tokyo, Japan
| | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Sergei I Sukharev
- Department of Biology, University of Maryland, College Park, Maryland
| | - Thomas M Suchyna
- Department of Physiology and Biophysics, State University of New York, Buffalo, New York.
| |
Collapse
|
30
|
Goushcha A, Goloverda GZ, Kotsyuba O, Perepichka DF, Seumenicht O, Ladokhin AS. Crimea report leaves readers in the cold. Science 2016; 352:780-1. [DOI: 10.1126/science.aaf9663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
31
|
Vasquez-Montes V, Kyrychenko A, Rodnin MV, White SH, Ulmschneider MB, Ladokhin AS. Interplay between Hydrophobic and Electrostatic Interactions in Protonation-Dependent Insertion of Transmembrane Helices. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
32
|
Flores-Canales JC, Vargas-Uribe M, Ladokhin AS, Kurnikova M. Membrane Association of the Diphtheria Toxin Translocation Domain Studied by Coarse-Grained Simulations and Experiment. J Membr Biol 2015; 248:529-43. [PMID: 25650178 DOI: 10.1007/s00232-015-9771-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/02/2015] [Indexed: 12/01/2022]
Abstract
Diphtheria toxin translocation (T) domain inserts in lipid bilayers upon acidification of the environment. Computational and experimental studies have suggested that low pH triggers a conformational change of the T-domain in solution preceding membrane binding. The refolded membrane-competent state was modeled to be compact and mostly retain globular structure. In the present work, we investigate how this refolded state interacts with membrane interfaces in the early steps of T-domain's membrane association. Coarse-grained molecular dynamics simulations suggest two distinct membrane-bound conformations of the T-domain in the presence of bilayers composed of a mixture of zwitteronic and anionic phospholipids (POPC:POPG with a 1:3 molar ratio). Both membrane-bound conformations show a common near parallel orientation of hydrophobic helices TH8-TH9 relative to the membrane plane. The most frequently observed membrane-bound conformation is stabilized by electrostatic interactions between the N-terminal segment of the protein and the membrane interface. The second membrane-bound conformation is stabilized by hydrophobic interactions between protein residues and lipid acyl chains, which facilitate deeper protein insertion in the membrane interface. A theoretical estimate of a free energy of binding of a membrane-competent T-domain to the membrane is provided.
Collapse
|
33
|
Eells R, Heinirch F, Lösche M, Rodnin MV, Ladokhin AS. pH-Induced Reorganization and Membrane Insertion of the Diphtheria Toxin T-Domain Studied by Spr and Neutron Reflectometry. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
34
|
Li J, Rodnin MV, Ladokhin AS, Gross ML. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain. Biochemistry 2014; 53:6849-56. [PMID: 25290210 PMCID: PMC4222528 DOI: 10.1021/bi500893y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.
Collapse
Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
| | | | | | | |
Collapse
|
35
|
Rodnin MV, Ladokhin AS. Membrane translocation assay based on proteolytic cleavage: application to diphtheria toxin T domain. Biochim Biophys Acta 2014; 1848:35-40. [PMID: 25291602 DOI: 10.1016/j.bbamem.2014.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
The function of diphtheria toxin translocation (T) domain is to transfer the catalytic domain across the endosomal membrane upon acidification. The goal of this study was to develop and apply an in vitro functional assay for T domain activity, suitable for investigation of structure-function relationships of translocation across lipid bilayers of various compositions. Traditionally, T domain activity in vitro is estimated by measuring either conductance in planar lipid bilayers or the release of fluorescent markers from lipid vesicles. While an in vivo cell death assay is the most relevant to physiological function, it cannot be applied to studying the effects of pH or membrane lipid composition on translocation. Here we suggest an assay based on cleavage of the N-terminal part of T domain upon translocation into protease-loaded vesicles. A series of control experiment was used to confirm that cleavage occurs inside the vesicle and not as the result of vesicle disruption. Translocation of the N-terminus of the T domain is shown to require the presence of a critical fraction of anionic lipids, which is consistent with our previous biophysical measurements of insertion. Application of the proposed assay to a series of T domain mutants correlated well with the results of cytotoxicity assay.
Collapse
Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States.
| |
Collapse
|
36
|
Vargas-Uribe M, Rodnin MV, Öjemalm K, Holgado A, Kyrychenko A, Nilsson I, Posokhov YO, Makhatadze G, von Heijne G, Ladokhin AS. Thermodynamics of Membrane Insertion and Refolding of the Diphtheria Toxin T-Domain. J Membr Biol 2014; 248:383-94. [PMID: 25281329 DOI: 10.1007/s00232-014-9734-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/23/2014] [Indexed: 11/26/2022]
Abstract
The diphtheria toxin translocation (T) domain inserts into the endosomal membrane in response to the endosomal acidification and enables the delivery of the catalytic domain into the cell. The insertion pathway consists of a series of conformational changes that occur in solution and in the membrane and leads to the conversion of a water-soluble state into a transmembrane state. In this work, we utilize various biophysical techniques to characterize the insertion pathway from the thermodynamic perspective. Thermal and chemical unfolding measured by differential scanning calorimetry, circular dichroism, and tryptophan fluorescence reveal that the free energy of unfolding of the T-domain at neutral and mildly acidic pH differ by 3-5 kcal/mol, depending on the experimental conditions. Fluorescence correlation spectroscopy measurements show that the free energy change from the membrane-competent state to the interfacial state is approximately -8 kcal/mol and is pH-independent, while that from the membrane-competent state to the transmembrane state ranges between -9.5 and -12 kcal/mol, depending on the membrane lipid composition and pH. Finally, the thermodynamics of transmembrane insertion of individual helices was tested using an in vitro assay that measures the translocon-assisted integration of test sequences into the microsomal membrane. These experiments suggest that even the most hydrophobic helix TH8 has only a small favorable free energy of insertion. The free energy for the insertion of the consensus insertion unit TH8-TH9 is slightly more favorable, yet less favorable than that measured for the entire protein, suggesting a cooperative effect for the membrane insertion of the helices of the T-domain.
Collapse
Affiliation(s)
- Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Kyrychenko A, Freites JA, He J, Tobias DJ, Wimley WC, Ladokhin AS. Structural plasticity in the topology of the membrane-interacting domain of HIV-1 gp41. Biophys J 2014; 106:610-20. [PMID: 24507601 DOI: 10.1016/j.bpj.2013.12.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 12/17/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022] Open
Abstract
We use a number of computational and experimental approaches to investigate the membrane topology of the membrane-interacting C-terminal domain of the HIV-1 gp41 fusion protein. Several putative transmembrane regions are identified using hydrophobicity analysis based on the Wimley-White scales, including the membrane-proximal external region (MPER). The MPER region is an important target for neutralizing anti-HIV monoclonal antibodies and is believed to have an interfacial topology in the membrane. To assess the possibility of a transmembrane topology of MPER, we examined the membrane interactions of a peptide corresponding to a 22-residue stretch of the MPER sequence (residues 662-683) using fluorescence spectroscopy and oriented circular dichroism. In addition to the previously reported interfacial location, we identify a stable transmembrane conformation of the peptide in synthetic lipid bilayers. All-atom molecular dynamics simulations of the MPER-derived peptide in a lipid bilayer demonstrate a stable helical structure with an average tilt of 24 degrees, with the five tryptophan residues sampling different environments inside the hydrocarbon core of the lipid bilayer, consistent with the observed spectral properties of intrinsic fluorescence. The degree of lipid bilayer penetration obtained by computer simulation was verified using depth-dependent fluorescence quenching of a selectively attached fluorescence probe. Overall, our data indicate that the MPER sequence can have at least two stable conformations in the lipid bilayer, interfacial and transmembrane, and suggest a possibility that external perturbations can switch the topology during physiological functioning.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, California
| | - Jing He
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, California
| | - William C Wimley
- Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas.
| |
Collapse
|
38
|
Ladokhin AS. Measuring membrane penetration with depth-dependent fluorescence quenching: distribution analysis is coming of age. Biochim Biophys Acta 2014; 1838:2289-95. [PMID: 24593994 DOI: 10.1016/j.bbamem.2014.02.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
Depth-dependent fluorescence quenching by lipid-attached quenchers (e.g., bromine atoms and doxyl groups) is an important tool for determining the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information and accurate calculations of the depth of the fluorophore are complicated by thermal disorder, resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Twenty-one years ago a methodology called distribution analysis (DA) was introduced, based on the emerging view of the complexity of the transverse organization of lipid bilayer structure. The method is aimed at extracting quantitative information on membrane penetration, such as position and width of fluorophore's distribution along the depth coordinate and its exposure to the lipid phase. Here we review recent progress in refining the DA method and illustrate its applications to protein-membrane interactions. We demonstrate how basic assumptions of the DA approach can be validated using molecular dynamics simulations and how the precision of depth determination is improved by applying a new protocol based on a combination of steady-state and time-resolved fluorescence quenching. Using the example of the MPER fragment of the membrane-spanning domain of the HIV-1 gp41 fusion protein, we illustrate how DA applications and computer simulations can be used together to reveal the molecular organization of a protein-membrane complex. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
Collapse
Affiliation(s)
- Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, USA.
| |
Collapse
|
39
|
Vargas-Uribe M, Rodnin MV, Kienker P, Finkelstein A, Ladokhin AS. Crucial Role of H322 in the Folding of Diphtheria Toxin T-Domain into the Open-Channel State. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
40
|
Ghatak C, Rodnin MV, Öjemalm K, Holgado A, Vargas-Uribe M, Nilsson I, von Heijne G, Ladokhin AS. Do Acidic Residues in TH8-TH9 Play a Role in Transmembrane Insertion of the Diphtheria Toxin T-Domain? Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
41
|
Kyrychenko A, He J, Wimley WC, Ladokhin AS. Structural Plasticity in the Topology of Membrane-Spanning Domain of HIV-1 gp41. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
42
|
Vargas-Uribe M, Ladokhin AS. Membrane Insertion Pathway of the Apoptotic Repressor Bcl-xL: How (DIS)Similar is it to that of Diphtheria Toxin T-Domain? Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
43
|
Kyrychenko A, Rodnin MV, Tobias DJ, Ladokhin AS. Refining Analysis of Membrane Penetration with Depth-Dependent Fluorescence Quenching and Molecular Dynamics Simulations. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
44
|
Ladokhin AS, Holloway PW, Kostrzhevska EG. Distribution analysis of membrane penetration of proteins by depth-dependent fluorescence quenching. J Fluoresc 2013; 3:195-7. [PMID: 24234833 DOI: 10.1007/bf00862742] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/1993] [Indexed: 10/26/2022]
Abstract
A new approach is presented to evaluate the depth-dependent quenching of the fluorescence of membrane-bound probes and integral proteins. By utilizing at least three quenchers of known and distinctly different depths, the following parameters can be recovered: most probable depth of the probe; dispersion of the depth distribution, which will depend on the size of probe and fluctuations in its position; and quenching efficiency, which is related to the exposure of a particular fluorophore to the lipid phase. The exposure of tryptophan residues in integral proteins can be quantitatively determined with respect to the model compound (tryptophan octyl ester). The proposed method was applied to the investigation of membrane complexes of the bee venom melittin and cytochrome b5.
Collapse
Affiliation(s)
- A S Ladokhin
- Biology Department and McCollum-Pratt Institute, The Johns Hopkins University, 21218, Baltimore, Maryland
| | | | | |
Collapse
|
45
|
Vargas-Uribe M, Rodnin MV, Ladokhin AS. Comparison of membrane insertion pathways of the apoptotic regulator Bcl-xL and the diphtheria toxin translocation domain. Biochemistry 2013; 52:7901-9. [PMID: 24134052 DOI: 10.1021/bi400926k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The diphtheria toxin translocation domain (T-domain) and the apoptotic repressor Bcl-xL are membrane proteins that adopt their final topology by switching folds from a water-soluble to a membrane-inserted state. While the exact molecular mechanisms of this transition are not clearly understood in either case, the similarity in the structures of soluble states of the T-domain and Bcl-xL led to the suggestion that their membrane insertion pathways will be similar, as well. Previously, we have applied an array of spectroscopic methods to characterize the pH-triggered refolding and membrane insertion of the diphtheria toxin T-domain. Here, we use the same set of methods to describe the membrane insertion pathway of Bcl-xL, which allows us to make a direct comparison between both systems with respect to the thermodynamic stability in solution, pH-dependent membrane association, and transmembrane insertion. Thermal denaturation measured by circular dichroism indicates that, unlike the T-domain, Bcl-xL does not undergo a pH-dependent destabilization of the structure. Förster resonance energy transfer measurements demonstrate that Bcl-xL undergoes reversible membrane association modulated by the presence of anionic lipids, suggesting that formation of the membrane-competent form occurs close to the membrane interface. Membrane insertion of the main hydrophobic helical hairpin of Bcl-xL, α5-α6, was studied by site-selective attachment of environment-sensitive dye NBD. In contrast to the insertion of the corresponding TH8-TH9 hairpin into the T-domain, insertion of α5-α6 was found not to depend strongly on the presence of anionic lipids. Taken together, our results indicate that while Bcl-xL and the T-domain share structural similarities, their modes of conformational switching and membrane insertion pathways are distinctly different.
Collapse
Affiliation(s)
- Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | | | | |
Collapse
|
46
|
Kyrychenko A, Ladokhin AS. Refining membrane penetration by a combination of steady-state and time-resolved depth-dependent fluorescence quenching. Anal Biochem 2013; 446:19-21. [PMID: 24141077 DOI: 10.1016/j.ab.2013.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022]
Abstract
Accurate determination of the depth of membrane penetration of a fluorescent probe, attached to a lipid, protein, or other macromolecule of interest, using depth-dependent quenching methodology is complicated by thermal motion in the lipid bilayer. Here, we suggest that a combination of steady-state and time-resolved measurements can be used to generate a static quenching profile that reduces the contribution from transverse diffusion occurring during the excited-state lifetime. This procedure results in narrower quenching profiles, compared with those obtained by traditional measurements, and thus improves precision in determination of the underlying depth distribution of the probe.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA.
| |
Collapse
|
47
|
Vargas-Uribe M, Rodnin MV, Kienker P, Finkelstein A, Ladokhin AS. Crucial role of H322 in folding of the diphtheria toxin T-domain into the open-channel state. Biochemistry 2013; 52:3457-63. [PMID: 23621842 DOI: 10.1021/bi400249f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The translocation (T) domain plays a key role in the entry of diphtheria toxin into the cell. Upon endosomal acidification, the T-domain undergoes a series of conformational changes that lead to its membrane insertion and formation of a channel. Recently, we have reported that the triple replacement of C-terminal histidines H322, H323, and H372 with glutamines prevents the formation of open channels in planar lipid bilayers. Here, we report that this effect is primarily due to the mutation of H322. We further examine the relationship between the loss of functionality and membrane folding in a series of mutants with C-terminal histidine substitutions using spectroscopic assays. The membrane insertion pathway for the mutants differs from that of the wild type as revealed by the membrane-induced red shift of tryptophan fluorescence at pH 6.0-6.5. T-Domain mutants with replacements at H323 and H372, but not at H322, regain a wild-type-like spectroscopic signature upon further acidification. Circular dichroism measurements confirm that affected mutants misfold during insertion into vesicles. Conductance measurements reveal that substituting H322 dramatically reduces the numbers of properly folded channels in a planar bilayer, but the properties of the active channels appear to be unaltered. We propose that H322 plays an important role in the formation of open channels and is involved in guiding the proper insertion of the N-terminal region of the T-domain into the membrane.
Collapse
Affiliation(s)
- Mauricio Vargas-Uribe
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | | | | | | | | |
Collapse
|
48
|
Kyrychenko A, Ladokhin AS. Molecular dynamics simulations of depth distribution of spin-labeled phospholipids within lipid bilayer. J Phys Chem B 2013; 117:5875-85. [PMID: 23614631 DOI: 10.1021/jp4026706] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spin-labeled lipids are commonly used as fluorescence quenchers in studies of membrane penetration of dye-labeled proteins and peptides using depth-dependent quenching. Accurate calculations of depth of the fluorophore rely on the use of several spin labels placed in the membrane at various positions. The depth of the quenchers (spin probes) has to be determined independently; however, experimental determination of transverse distributions of spin probe depths is difficult. In this Article, we use molecular dynamics (MD) simulations to study the membrane behavior and depth distributions of spin-labeled phospholipids in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. To probe different depths within the bilayer, a series containing five Doxyl-labeled lipids (n-Doxyl PC) has been studied, in which a spin moiety was covalently attached to nth carbon atoms (where n = 5, 7, 10, 12, and 14) of the sn-2 stearoyl chain of the host phospholipid. Our results demonstrate that the chain-attached spin labels are broadly distributed across the model membrane and their environment is characterized by a high degree of mobility and structural heterogeneity. Despite the high thermal disorder, the depth distributions of the Doxyl labels were found to correlate well with their attachment positions, indicating that the distribution of the spin label within the model membrane is dictated by the depth of the nth lipid carbon atom and not by intrinsic properties of the label. In contrast, a much broader and heterogeneous distribution was observed for a headgroup-attached Tempo spin label of Tempo-PC lipids. MD simulations reveal that, due to the hydrophobic nature, a Tempo moiety favors partitioning from the headgroup region deeper into the membrane. Depending on the concentration of Tempo-PC lipids, the probable depth of the Tempo moiety could span a range from 14.4 to 18.2 Å from the membrane center. Comparison of the MD-estimated immersion depths of Tempo and n-Doxyl labels with their suggested experimental depth positions allows us to review critically the possible sources of error in depth-dependent fluorescence quenching studies.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160-7421, USA.
| | | |
Collapse
|
49
|
Kurnikov IV, Kyrychenko A, Flores-Canales JC, Rodnin MV, Simakov N, Vargas-Uribe M, Posokhov YO, Kurnikova M, Ladokhin AS. pH-triggered conformational switching of the diphtheria toxin T-domain: the roles of N-terminal histidines. J Mol Biol 2013; 425:2752-64. [PMID: 23648837 DOI: 10.1016/j.jmb.2013.04.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/13/2013] [Accepted: 04/27/2013] [Indexed: 01/28/2023]
Abstract
pH-induced conformational switching is essential for functioning of diphtheria toxin, which undergoes a membrane insertion/translocation transition triggered by endosomal acidification as a key step of cellular entry. In order to establish the sequence of molecular rearrangements and side-chain protonation accompanying the formation of the membrane-competent state of the toxin's translocation (T) domain, we have developed and applied an integrated approach that combines multiple techniques of computational chemistry [e.g., long-microsecond-range, all-atom molecular dynamics (MD) simulations; continuum electrostatics calculations; and thermodynamic integration (TI)] with several experimental techniques of fluorescence spectroscopy. TI calculations indicate that protonation of H257 causes the greatest destabilization of the native structure (6.9 kcal/mol), which is consistent with our early mutagenesis results. Extensive equilibrium MD simulations with a combined length of over 8 μs demonstrate that histidine protonation, while not accompanied by the loss of structural compactness of the T-domain, nevertheless results in substantial molecular rearrangements characterized by the partial loss of secondary structure due to unfolding of helices TH1 and TH2 and the loss of close contact between the C- and N-terminal segments. The structural changes accompanying the formation of the membrane-competent state ensure an easier exposure of the internal hydrophobic hairpin formed by helices TH8 and TH9, in preparation for its subsequent transmembrane insertion.
Collapse
Affiliation(s)
- Igor V Kurnikov
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Kyrychenko A, Tobias DJ, Ladokhin AS. Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer. J Phys Chem B 2013; 117:4770-8. [PMID: 23528135 PMCID: PMC3652981 DOI: 10.1021/jp310638f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Depth-dependent fluorescence quenching is an important tool for studying the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information from quenching data is, however, complicated by (1) a limited number of experimentally available quenchers and (2) thermal disorder resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Here we validate and refine a general approach to determining the location of a fluorescent probe along the bilayer normal from quenching data, based on a molecular dynamics (MD) simulation of a model compound, tryptophan octyl ester (TOE), in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The TOE ring was found to lie deeply within the bilayer (most probable position of 13.3 Å and center-of-weight of the distribution of 14.8 Å from the bilayer center), and it was very broadly distributed (with 9 Å depth distribution width), which is consistent with previous experimental observations. The depth-dependent quenching profiles were simulated by treating carbon atoms of the lipid acyl chain of POPC as "pseudo-quenchers" and calculating appropriate transverse overlaps and collision rates with indole atoms of TOE. These simulated quenching profiles were well fitted by a Gaussian function of depth, as is routinely done with experimental data subjected to the distribution analysis procedure [Methods Enzymol. 1997, 278, 462-473]. Comparison of the collisional pseudoquenching profiles with the actual profiles of the indole moiety of TOE allows for testing of the validity of the data analysis and identification of the possible sources of error in calculating depths of membrane penetration from quenching data.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, CA 92697-2025, U.S.A
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160-7421, U.S.A
| |
Collapse
|