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Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates. Angew Chem Int Ed Engl 2023; 62:e202303943. [PMID: 37170337 PMCID: PMC10592574 DOI: 10.1002/anie.202303943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.
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Affiliation(s)
- Alex Nazzaro
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Brandon Lu
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | | | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
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2
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Pal S. Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
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3
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Di Silvio S, Bologna F, Milli L, Giuri D, Zanna N, Castellucci N, Monari M, Calvaresi M, Górecki M, Angelici G, Tomasini C, Pescitelli G. Elusive π-helical peptide foldamers spotted by chiroptical studies. Org Biomol Chem 2020; 18:865-877. [PMID: 31845697 DOI: 10.1039/c9ob02313e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A series of oligomers containing alternate l-Ala and pGlu (pyroglutamic acid) both in the L and D form have been prepared and conformationally investigated by X-ray, NMR, UV/ECD, IR/VCD and molecular modelling. X-ray diffraction analysis was possible for the shortest oligomers LL-1 and LD-1. Molecular dynamics simulations of the oligomers demonstrated that the energy landscapes of the LL-series are broad. In contrast, the energy landscapes of the LD-series are characterized by well-defined minima corresponding to specific conformational structures. A single well-defined minimum exists in the energy landscape of the largest oligomer LD-8, corresponding to a precise conformation, characterized by i + 5 →i N-HO[double bond, length as m-dash]C hydrogen bonds, typical of a π-helix. ECD and VCD spectra were measured to identify the chiroptical profiles of the oligomers. The most striking element in the ECD spectra of the LD-series is their exceptionally strong intensity, which confirms that these polypeptides attain a high degree of helical order. VCD spectra for the LD-series are well reproduced by frequency calculations when π-helix folds are employed as input structures, suggesting that a symmetrical VCD couplet around 1720 cm-1 can be taken as the VCD signature of π-helices.
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Affiliation(s)
- Sergio Di Silvio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Fabio Bologna
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Lorenzo Milli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Demetra Giuri
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Nicola Zanna
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Nicola Castellucci
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Magda Monari
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Marcin Górecki
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy. and Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 01-224, Poland
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy.
| | - Claudia Tomasini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy.
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Abstract
Peptide secondary and tertiary structure motifs frequently serve as inspiration for the development of protein-protein interaction (PPI) inhibitors. While a wide variety of strategies have been used to stabilize or imitate α-helices, similar strategies for β-sheet stabilization are more limited. Synthetic scaffolds that stabilize reverse turns and cross-strand interactions have provided important insights into β-sheet stability and folding. However, these templates occupy regions of the β-sheet that might impact the β-sheet's ability to bind at a PPI interface. Here, we present the hydrogen bond surrogate (HBS) approach for stabilization of β-hairpin peptides. The HBS linkage replaces a cross-strand hydrogen bond with a covalent linkage, conferring significant conformational and proteolytic resistance. Importantly, this approach introduces the stabilizing linkage in the buried β-sheet interior, retains all side chains for further functionalization, and allows efficient solid-phase macrocyclization. We anticipate that HBS stabilization of PPI β-sheets will enhance the development of β-sheet PPI inhibitors and expand the repertoire of druggable PPIs.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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5
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Pal S, Prabhakaran EN. Hydrogen bond surrogate stabilized water soluble 310-helix from a disordered pentapeptide containing coded α-amino acids. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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6
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Notter RH, Wang Z, Walther FJ. Activity and biophysical inhibition resistance of a novel synthetic lung surfactant containing Super-Mini-B DATK peptide. PeerJ 2016; 4:e1528. [PMID: 26793419 PMCID: PMC4715451 DOI: 10.7717/peerj.1528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/02/2015] [Indexed: 12/22/2022] Open
Abstract
Background/objectives. This study examines the surface activity, resistance to biophysical inhibition, and pulmonary efficacy of a synthetic lung surfactant containing glycerophospholipids combined with Super Mini-B (S-MB) DATK, a novel and stable molecular mimic of lung surfactant protein (SP)-B. The objective of the work is to test whether S-MB DATK synthetic surfactant has favorable biophysical and physiological activity for future use in treating surfactant deficiency or dysfunction in lung disease or injury. Methods. The structure of S-MB DATK peptide was analyzed by homology modeling and by FTIR spectroscopy. The in vitro surface activity and inhibition resistance of synthetic S-MB DATK surfactant was assessed in the presence and absence of albumin, lysophosphatidylcholine (lyso-PC), and free fatty acids (palmitoleic and oleic acid). Adsorption and dynamic surface tension lowering were measured with a stirred subphase dish apparatus and a pulsating bubble surfactometer (20 cycles/min, 50% area compression, 37 °C). In vivo pulmonary activity of S-MB DATK surfactant was measured in ventilated rabbits with surfactant deficiency/dysfunction induced by repeated lung lavages that resulted in arterial PO2 values <100 mmHg. Results. S-MB DATK surfactant had very high surface activity in all assessments. The preparation adsorbed rapidly to surface pressures of 46–48 mN/m at 37 °C (low equilibrium surface tensions of 22–24 mN/m), and reduced surface tension to <1 mN/m under dynamic compression on the pulsating bubble surfactometer. S-MB DATK surfactant showed a significant ability to resist inhibition by serum albumin, C16:0 lyso-PC, and free fatty acids, but surfactant inhibition was mitigated by increasing surfactant concentration. S-MB DATK synthetic surfactant quickly improved arterial oxygenation and lung compliance after intratracheal instillation to ventilated rabbits with severe surfactant deficiency. Conclusions. S-MB DATK is an active mimic of native SP-B. Synthetic surfactants containing S-MB DATK (or related peptides) combined with lipids appear to have significant future potential for treating clinical states of surfactant deficiency or dysfunction, such as neonatal and acute respiratory distress syndromes.
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Affiliation(s)
- Robert H Notter
- Department of Pediatrics, University of Rochester , Rochester, NY , United States
| | - Zhengdong Wang
- Department of Pediatrics, University of Rochester , Rochester, NY , United States
| | - Frans J Walther
- Department of Pediatrics, David Geffen School of Medicine, University of California , Los Angeles, CA , United States
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7
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Kumar P, Bansal M. Dissecting π-helices: sequence, structure and function. FEBS J 2015; 282:4415-32. [DOI: 10.1111/febs.13507] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/26/2015] [Accepted: 09/02/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Prasun Kumar
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
| | - Manju Bansal
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
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8
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Kosower EM, Borz G. N-alkylacylamides in thin films display infrared spectra of 3₁₀-, α-, and π-helices with visible static and dynamic growth phases. Chemphyschem 2014; 15:3598-607. [PMID: 25113617 DOI: 10.1002/cphc.201402325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/18/2014] [Indexed: 11/10/2022]
Abstract
A peptide model is a physical system containing a CONH group, the simplest being HCONHCH3 , N-methylformamide (NMF). We have discovered that NMF and N-methylacetamide (NMA), which form hydrogen-bonded oligomers in thin films on a planar AgX fiber, display infrared (IR) spectra with peaks like those of polypeptide helices. Structures can be assigned by their amide I maxima near 1672 (3(10)), 1655 (3(10)), 1653 (α), 1655 (π), and 1635 cm(-1) (π), which are the first IR data for the π-helix. Sharp peaks are an outcome of immobilization of polar species on the polar surface of silver halides. We report the first use of expanded thin-film IR spectroscopy, in which plots of every spectrum over the amide I-II range show pauses or slow stages in the increase or decrease of absorption. These are identified as static phases followed by dynamic phases, with the incremental gain or loss of a helix turn. A general theory can be stated for such processes. Density functional calculations show that the NMA α-helix pentamer (crystal structure geometry) is transformed into a π-helix-like form. For the first time, an entire sequence (3(10)-helix, α-helix, π-helix, quasiplanar species) of spectra has been recorded for NMA.
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Affiliation(s)
- Edward M Kosower
- School of Chemistry, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978 (Israel).
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9
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Kosower EM, Borz G, Goldberg I, Ermakov N. N-methyl-trimethylacetamide in thin films displays infrared spectra of π-helices, with visible static and dynamic growth phases, and then a β-sheet. Chemphyschem 2014; 15:3592-7. [PMID: 25113777 DOI: 10.1002/cphc.201402326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/18/2014] [Indexed: 11/09/2022]
Abstract
The simplest (minimal) peptide model is HCONHCH3. An increase in the π-helix content with increased substitution in the acyl portion suggested the examination of N-methyl-trimethylacetamide) (NMT). NMT displays spectra, in which there is evolution of a set of helices defined by their amide I maxima near 1686 (3(10)), 1655 (first π), and, most importantly, at 1637 cm(-1) (π). Expanded thin-film infrared spectroscopy (XTFIS) shows pauses or slow stages, which are identified as static phases followed by dynamic phases with the incremental gain or loss of a helix turn. In addition, absorbance at 1637 cm(-1) suddenly increases at 82.1 s (30% over 0.3 s), indicating a phase change and crystallization of the π-helix, along with a coincidental decrease in the absorbance for the first π-helix. A sharp peak occurs at the maximum of the phase change at 82.5 s, representing a pure NMT π-helix. The spectra then undergo a decreasing general absorption loss over 150 s, with the π-helix evolving further to an antiparallel β-sheet fragment. The spectral quality arises from the immobilization of polar molecules on polar surfaces. The crystal structure is that of an antiparallel β-sheet.
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Affiliation(s)
- Edward M Kosower
- School of Chemistry, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978 (Israel).
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10
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Walther FJ, Waring AJ, Hernández-Juviel JM, Ruchala P, Wang Z, Notter RH, Gordon LM. Surfactant protein C peptides with salt-bridges ("ion-locks") promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein. PeerJ 2014; 2:e485. [PMID: 25083348 PMCID: PMC4106191 DOI: 10.7717/peerj.485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/23/2014] [Indexed: 11/20/2022] Open
Abstract
Background. Surfactant protein C (SP-C; 35 residues) in lungs has a cationic N-terminal domain with two cysteines covalently linked to palmitoyls and a C-terminal region enriched in Val, Leu and Ile. Native SP-C shows high surface activity, due to SP-C inserting in the bilayer with its cationic N-terminus binding to the polar headgroup and its hydrophobic C-terminus embedded as a tilted, transmembrane α-helix. The palmitoylcysteines in SP-C act as ‘helical adjuvants’ to maintain activity by overriding the β-sheet propensities of the native sequences. Objective. We studied SP-C peptides lacking palmitoyls, but containing glutamate and lysine at 4-residue intervals, to assess whether SP-C peptides with salt-bridges (“ion-locks”) promote surface activity by mimicking the α-helix and membrane topography of native SP-C. Methods. SP-C mimics were synthesized that reproduce native sequences, but without palmitoyls (i.e., SP-Css or SP-Cff, with serines or phenylalanines replacing the two cysteines). Ion-lock SP-C molecules were prepared by incorporating single or double Glu−–Lys+ into the parent SP-C’s. The secondary structures of SP-C mimics were studied with Fourier transform infrared (FTIR) spectroscopy and PASTA, an algorithm that predicts β-sheet propensities based on the energies of the various β-sheet pairings. The membrane topography of SP-C mimics was investigated with orientated and hydrogen/deuterium (H/D) exchange FTIR, and also Membrane Protein Explorer (MPEx) hydropathy analysis. In vitro surface activity was determined using adsorption surface pressure isotherms and captive bubble surfactometry, and in vivo surface activity from lung function measures in a rabbit model of surfactant deficiency. Results. PASTA calculations predicted that the SP-Css and SP-Cff peptides should each form parallel β-sheet aggregates, with FTIR spectroscopy confirming high parallel β-sheet with ‘amyloid-like’ properties. The enhanced β-sheet properties for SP-Css and SP-Cff are likely responsible for their low surfactant activities in the in vitro and in vivo assays. Although standard 12C-FTIR study showed that the α-helicity of these SP-C sequences in lipids was uniformly increased with Glu−–Lys+ insertions, elevated surfactant activity was only selectively observed. Additional results from oriented and H/D exchange FTIR experiments indicated that the high surfactant activities depend on the SP-C ion-locks recapitulating both the α-helicity and the membrane topography of native SP-C. SP-Css ion-lock 1, an SP-Css with a salt-bridge for a Glu−–Lys+ ion-pair predicted from MPEx hydropathy calculations, demonstrated enhanced surfactant activity and a transmembrane helix simulating those of native SP-C. Conclusion. Highly active SP-C mimics were developed that replace the palmitoyls of SP-C with intrapeptide salt-bridges and represent a new class of synthetic surfactants with therapeutic interest.
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Affiliation(s)
- Frans J Walther
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America ; Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America
| | - Alan J Waring
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America ; Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America ; Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America ; Department of Physiology & Biophysics, School of Medicine, University of California , Irvine, CA , United States of America
| | - José M Hernández-Juviel
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America
| | - Piotr Ruchala
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America
| | - Zhengdong Wang
- Department of Pediatrics, University of Rochester , Rochester, NY , United States of America
| | - Robert H Notter
- Department of Pediatrics, University of Rochester , Rochester, NY , United States of America
| | - Larry M Gordon
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America
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Thorat VH, Ingole TS, Vijayadas KN, Nair RV, Kale SS, Ramesh VVE, Davis HC, Prabhakaran P, Gonnade RG, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. The Ant-Pro Reverse-Turn Motif. Structural Features and Conformational Characteristics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Truncated and helix-constrained peptides with high affinity and specificity for the cFos coiled-coil of AP-1. PLoS One 2013; 8:e59415. [PMID: 23544065 PMCID: PMC3609778 DOI: 10.1371/journal.pone.0059415] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/14/2013] [Indexed: 01/20/2023] Open
Abstract
Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i→i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, α-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable α-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ∼9 kcal/mol, but this was compensated by increased conformational entropy (TΔS ≤7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by α-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases.
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13
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Vijayadas KN, Nair RV, Gawade RL, Kotmale AS, Prabhakaran P, Gonnade RG, Puranik VG, Rajamohanan PR, Sanjayan GJ. Ester vs. amide on folding: a case study with a 2-residue synthetic peptide. Org Biomol Chem 2013; 11:8348-56. [DOI: 10.1039/c3ob41967c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Basuroy K, Dinesh B, Shamala N, Balaram P. Structural Characterization of Backbone-Expanded Helices in Hybrid Peptides: (αγ)n and (αβ)n Sequences with Unconstrained β and γ Homologues of L-Val. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204436] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Basuroy K, Dinesh B, Shamala N, Balaram P. Structural Characterization of Backbone-Expanded Helices in Hybrid Peptides: (αγ)n and (αβ)n Sequences with Unconstrained β and γ Homologues of L-Val. Angew Chem Int Ed Engl 2012; 51:8736-9. [DOI: 10.1002/anie.201204436] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Indexed: 12/26/2022]
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16
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Abstract
Oligomers composed of β(3)-amino acid residues and a mixture of α- and β(3)-residues have emerged as proteolytically stable structural mimics of α-helices. An attractive feature of these oligomers is that they adopt defined conformations in short sequences. In this manuscript, we evaluate the impact of β(3)-residues as compared to their α-amino acid analogs in prenucleated helices. Our hydrogen-deuterium exchange results suggest that heterogeneous sequences composed of "αααβ" repeats are conformationally more rigid than the corresponding homogeneous α-peptide helices, with the macrocycle templating the helical conformation having a significant influence.
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Affiliation(s)
- Anupam Patgiri
- Department of Chemistry, New York University, New York, New York 10003, USA
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17
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Xiong K, Asher SA. Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics. J Phys Chem B 2012; 116:7102-12. [PMID: 22612556 PMCID: PMC3381074 DOI: 10.1021/jp302007g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO(4)(-) binding to the Lys side chain -NH(3)(+) groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO(4)(-) binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
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18
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Mahon AB, Arora PS. Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices. Chem Commun (Camb) 2012; 48:1416-8. [PMID: 21952530 PMCID: PMC3412876 DOI: 10.1039/c1cc14730g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Appropriately-placed hydrogen bond surrogates have been demonstrated to efficiently nucleate helical conformations. Herein we describe an efficient method for the synthesis of thioether-based hydrogen bond surrogate (teHBS) helices. A teHBS helix is shown to adopt a stable conformation and target its cognate protein receptor with high affinity.
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Affiliation(s)
- Andrew B Mahon
- Department of Chemistry, New York University, New York, NY 10003, USA
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Mahon AB, Miller SE, Joy ST, Arora PS. Rational Design Strategies for Developing Synthetic Inhibitors of Helical Protein Interfaces. TOPICS IN MEDICINAL CHEMISTRY 2012. [DOI: 10.1007/978-3-642-28965-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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20
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic Structural Parameters for the γ-Peptide 14-Helix: Importance of Subunit Preorganization. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101301] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic structural parameters for the γ-peptide 14-helix: importance of subunit preorganization. Angew Chem Int Ed Engl 2011; 50:5843-6. [PMID: 21567680 DOI: 10.1002/anie.201101301] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI 53706, USA
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22
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Dunkin CM, Pokorny A, Almeida PF, Lee HS. Molecular dynamics studies of transportan 10 (tp10) interacting with a POPC lipid bilayer. J Phys Chem B 2011; 115:1188-98. [PMID: 21194203 PMCID: PMC3039315 DOI: 10.1021/jp107763b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed a series of molecular dynamics simu lations to study the nature of interactions between transportan 10 (tp10) and a zwitterionic POPC bilayer. Tp10 is an amphipathic cell-penetrating peptide with a net positive charge of +5 and is known to adopt an α-helical secondary structure on the surface of POPC membranes. The study showed that tp10 preferentially binds to the membrane surface with its hydrophobic side facing the hydrophobic lipid core. Such orientation allows Lys residues, with positively charged long side chains, to stay in the polar environment during the insertion process. The simulations revealed that the Lys-phosphate salt bridge is a key factor in determining the orientation of the peptide in the interfacial region as well as in stabilizing the peptide-membrane interaction. The electrostatic attraction between Lys and phosphate groups is also believed to be the main bottleneck for the translocation of tp10 across the membrane.
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Affiliation(s)
- Christina M. Dunkin
- Dept. of Chemistry and Biochemistry, University of North Carolina, Wilmington NC 28403
| | - Antje Pokorny
- Dept. of Chemistry and Biochemistry, University of North Carolina, Wilmington NC 28403
| | - Paulo F. Almeida
- Dept. of Chemistry and Biochemistry, University of North Carolina, Wilmington NC 28403
| | - Hee-Seung Lee
- Dept. of Chemistry and Biochemistry, University of North Carolina, Wilmington NC 28403
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23
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Liu F, Giubellino A, Simister PC, Qian W, Giano MC, Feller SM, Bottaro DP, Burke TR. Application of ring-closing metathesis to Grb2 SH3 domain-binding peptides. Biopolymers 2011; 96:780-8. [PMID: 21830199 PMCID: PMC3402909 DOI: 10.1002/bip.21692] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structure commonly involved with cellular signal transduction. However, unlike -helices, for which a substantial body of work exists regarding applications of ring-closing metathesis (RCM), there are few reports on the stabilization of PPII helices by RCM methodologies. The current study examined the effects of RCM macrocyclization on left-handed PPII helices involved with the SH3 domain-mediated binding of Sos1–Grb2. Starting with the Sos1-derived peptide “Ac-V1-P2-P3-P4-V5-P6-P7-R8-R9-R10-amide,” RCM macrocyclizations were conducted using alkenyl chains of varying lengths originating from the pyrrolidine rings of the Pro4 and Pro7 residues. The resulting macrocyclic peptides showed increased helicity as indicated by circular dichroism and enhanced abilities to block Grb2–Sos1 interactions in cell lysate pull-down assays. The synthetic approach may be useful in RCM macrocyclizations, where maintenance of proline integrity at both ring junctures is desired.
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Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Alessio Giubellino
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Philip C. Simister
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Wenjian Qian
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Michael C. Giano
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Stephan M. Feller
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Donald P. Bottaro
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
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24
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Pérez de Vega MJ, García-Aranda MI, González-Muñiz R. A role for ring-closing metathesis in medicinal chemistry: Mimicking secondary architectures in bioactive peptides. Med Res Rev 2010; 31:677-715. [DOI: 10.1002/med.20199] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Liu F, Stephen AG, Waheed AA, Freed EO, Fisher RJ, Burke TR. Application of ring-closing metathesis macrocyclization to the development of Tsg101-binding antagonists. Bioorg Med Chem Lett 2010; 20:318-21. [PMID: 19914066 PMCID: PMC2818493 DOI: 10.1016/j.bmcl.2009.10.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/23/2009] [Accepted: 10/26/2009] [Indexed: 11/18/2022]
Abstract
HIV-1 viral budding involves binding of the viral Gag(p6) protein to the ubiquitin E2 variant domain of the human tumor susceptibility gene 101 protein (Tsg101). Recognition of p6 by Tsg101 is mediated in part by a proline-rich motif that contains the sequence 'Pro-Thr-Ala-Pro' ('PTAP'). Using the p6-derived 9-mer sequence 'PEPTAPPEE', we had previously improved peptide binding affinity by employing N-alkylglycine ('peptoid') residues. The current study applies ring-closing metathesis macrocyclization strategies to Tsg101-binding peptide-peptoid hybrids as an approach to stabilize binding conformations and to observe the effects of such macrocyclization on Tsg101-binding affinity and bioavailability.
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Affiliation(s)
- Fa Liu
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Andrew G. Stephen
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc. NCI-Frederick, Frederick, MD 21702
| | - Abdul A. Waheed
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Eric O. Freed
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Robert J. Fisher
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc. NCI-Frederick, Frederick, MD 21702
| | - Terrence R. Burke
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
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Antharam VC, Elliott DW, Mills FD, Farver RS, Sternin E, Long JR. Penetration depth of surfactant peptide KL4 into membranes is determined by fatty acid saturation. Biophys J 2009; 96:4085-98. [PMID: 19450480 DOI: 10.1016/j.bpj.2008.12.3966] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 12/10/2008] [Accepted: 12/23/2008] [Indexed: 11/24/2022] Open
Abstract
KL(4) is a 21-residue functional peptide mimic of lung surfactant protein B, an essential protein for lowering surface tension in the alveoli. Its ability to modify lipid properties and restore lung compliance was investigated with circular dichroism, differential scanning calorimetry, and solid-state NMR spectroscopy. KL(4) binds fluid lamellar phase PC/PG lipid membranes and forms an amphipathic helix that alters lipid organization and acyl chain dynamics. The binding and helicity of KL(4) is dependent on the level of monounsaturation in the fatty acid chains. At physiologic temperatures, KL(4) is more peripheral and dynamic in fluid phase POPC/POPG MLVs but is deeply inserted into fluid phase DPPC/POPG vesicles, resulting in immobilization of the peptide. Substantial increases in the acyl chain order are observed in DPPC/POPG lipid vesicles with increasing levels of KL(4), and POPC/POPG lipid vesicles show small decreases in the acyl chain order parameters on addition of KL(4). Additionally, a clear effect of KL(4) on the orientation of the fluid phase PG headgroups is observed, with similar changes in both lipid environments. Near the phase transition temperature of the DPPC/POPG lipid mixtures, which is just below the physiologic temperature of lung surfactant, KL(4) causes phase separation with the DPPC remaining in a gel phase and the POPG partitioned between gel and fluid phases. The ability of KL(4) to differentially partition into lipid lamellae containing varying levels of monounsaturation and subsequent changes in curvature strain suggest a mechanism for peptide-mediated lipid organization and trafficking within the dynamic lung environment.
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Affiliation(s)
- Vijay C Antharam
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
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Vernall A, Cassidy P, Alewood P. A Single α-Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge. Angew Chem Int Ed Engl 2009; 48:5675-8. [DOI: 10.1002/anie.200901059] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Vernall A, Cassidy P, Alewood P. A Single α-Helical Turn Stabilized by Replacement of an Internal Hydrogen Bond with a Covalent Ethylene Bridge. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Antharam VC, Farver RS, Kuznetsova A, Sippel KH, Mills FD, Elliott DW, Sternin E, Long JR. Interactions of the C-terminus of lung surfactant protein B with lipid bilayers are modulated by acyl chain saturation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2544-54. [PMID: 18694722 DOI: 10.1016/j.bbamem.2008.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 07/02/2008] [Accepted: 07/17/2008] [Indexed: 01/14/2023]
Abstract
Lung surfactant protein B (SP-B) is critical to minimizing surface tension in the alveoli. The C-terminus of SP-B, residues 59-80, has much of the surface activity of the full protein and serves as a template for the development of synthetic surfactant replacements. The molecular mechanisms responsible for its ability to restore lung compliance were investigated with circular dichroism, differential scanning calorimetry, and (31)P and (2)H solid-state NMR spectroscopy. SP-B(59-80) forms an amphipathic helix which alters lipid organization and acyl chain dynamics in fluid lamellar phase 4:1 DPPC:POPG and 3:1 POPC:POPG MLVs. At higher levels of SP-B(59-80) in the POPC:POPG lipid system a transition to a nonlamellar phase is observed while DPPC:POPG mixtures remain in a lamellar phase. Deuterium NMR shows an increase in acyl chain order in DPPC:POPG MLVs on addition of SP-B(59-80); in POPC:POPG MLVs, acyl chain order parameters decrease. Our results indicate SP-B(59-80) penetrates deeply into DPPC:POPG bilayers and binds more peripherally to POPC:POPG bilayers. Similar behavior has been observed for KL(4), a peptide mimetic of SP-B which was originally designed using SP-B(59-80) as a template and has been clinically demonstrated to be successful in treating respiratory distress syndrome. The ability of these helical peptides to differentially partition into lipid lamellae based on their degree of monounsaturation and subsequent changes in lipid dynamics suggest a mechanism for lipid organization and trafficking within the dynamic lung environment.
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Affiliation(s)
- Vijay C Antharam
- Department of Biochemistry and Molecular Biology and McKnight Brain Institute, Box 100245, Gainesville, FL 32610-0245, USA
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