1
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Ghosh M, Gupta PK, Behera LM, Rana S. Structure of Designer Antibody-like Peptides Binding to the Human C5a with Potential to Modulate the C5a Receptor Signaling. J Med Chem 2024. [PMID: 39051153 DOI: 10.1021/acs.jmedchem.4c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
C5a is an integral glycoprotein of the complement system that plays an important role in inflammation and immunity. The physiological concentration of C5a is observed to be elevated under various immunoinflammatory pathophysiological conditions in humans. The pathophysiology of C5a is linked to the "two-site" protein-protein interactions (PPIs) with two genomically related receptors, such as C5aR1 and C5aR2. Therefore, pharmacophores that can potentially block the PPIs between C5a-C5aR1 and C5a-C5aR2 have tremendous potential for development as future therapeutics. Notably, the FDA has already approved antibodies that target the precursors of C5a (Eculizumab, 148 kDa) and C5a (Vilobelimab, 149 kDa) for marketing as complement-targeted therapeutics. In this context, the current study reports the structural characterization of a pair of synthetic designer antibody-like peptides (DePA and DePA1; ≤3.8 kDa) that bind to hotspot regions on C5a and also demonstrates potential traits to neutralize the function of C5a under pathophysiological conditions.
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Affiliation(s)
- Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
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2
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Lindner C, Friemel A, Schwegler N, Timmermann L, Pham TL, Reusche V, Kovermann M, Thomas F. Thermostable WW-Domain Scaffold to Design Functional β-Sheet Miniproteins. J Am Chem Soc 2024. [PMID: 38853610 DOI: 10.1021/jacs.4c03498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
There has been a recent surge in the design of miniproteins for medicinal chemistry, biomaterial design, or synthetic biology. In particular, there is an interest in peptide scaffolds that fold reliably, predictably, and with solid stability. In this article, we present the design of a highly thermostable WW domain, a three-stranded β-sheet motif, with a superior melting temperature of about 90 °C to serve as a core scaffold onto which receptor-like properties can be grafted. We have performed specific rounds of sequence iteration on a WW-domain consensus sequence to decipher sequence positions that affect structural and, thus, thermal stability. We identified a sequence-structure relationship that yields a highly thermostable WW-domain scaffold. High-resolution NMR spectroscopy was applied, which enabled the identification of structural features at the atomic scale that contribute to this high thermostability. Finally, we grafted the binding motifs of the three WW-domain groups─Group I, Group II/III, and Group IV─and organophosphate and metal binding onto the highly thermostable WW-domain scaffold and obtained thermostable de novo WW domains that indeed display the different binding modes that were intended. The organophosphate-binding WW domains exhibit melting temperatures that are up to 34 K higher than previously reported top-down designs. These results impressively demonstrate that the highly thermostable WW-domain core scaffold is a solid platform for the design of discrete and reliably folding functional β-sheet peptide miniproteins, providing an essential addition to the toolbox of peptide scaffolds previously used in synthetic biology and material design.
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Affiliation(s)
- Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Anke Friemel
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Niklas Schwegler
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Lisa Timmermann
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Vanessa Reusche
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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3
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Pellegrino S, Tonali N, Erba E, Kaffy J, Taverna M, Contini A, Taylor M, Allsop D, Gelmi ML, Ongeri S. β-Hairpin mimics containing a piperidine-pyrrolidine scaffold modulate the β-amyloid aggregation process preserving the monomer species. Chem Sci 2016; 8:1295-1302. [PMID: 28451272 PMCID: PMC5359901 DOI: 10.1039/c6sc03176e] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/05/2016] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease is a neurodegenerative disorder linked to oligomerization and fibrillization of amyloid β peptides, with Aβ1-42 being the most aggregative and neurotoxic one. We report herein the synthesis and conformational analysis of Aβ1-42-amyloid related β-hairpin peptidomimetics, built on a piperidine-pyrrolidine semi rigid β-turn inducer and bearing two small recognition peptide sequences, designed on oligomeric and fibril structures of Aβ1-42. According to these peptide sequences, a stable β-hairpin or a dynamic equilibrium between two possible architectures was observed. These original constructs are able to greatly delay the kinetics of Aβ1-42 aggregation process as demonstrated by thioflavin-T fluorescence, and transmission electron microscopy. Capillary electrophoresis indicates their ability to preserve the monomer species, inhibiting the formation of toxic oligomers. Furthermore, compounds protect against toxic effects of Aβ on neuroblastoma cells even at substoichiometric concentrations. This study is the first example of acyclic small β-hairpin mimics possessing such a highly efficient anti-aggregation activity. The protective effect is more pronounced than that observed with molecules which have undergone clinical trials. The structural elements made in this study provide valuable insights in the understanding of the aggregation process and insights to explore the design of novel acyclic β-hairpin targeting other types of amyloid-forming proteins.
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Affiliation(s)
- S Pellegrino
- DISFARM-Sez. Chimica Generale e Organica "A. Marchesini" , Universitá degli Studi di Milano , via Venezian 21 , 20133 Milano , Italy .
| | - N Tonali
- Molécules Fluorées et Chimie Médicinale , BioCIS , Univ. Paris-Sud , CNRS , Université Paris Saclay , 5 rue Jean-Baptiste Clément , 92296 Châtenay-Malabry Cedex , France .
| | - E Erba
- DISFARM-Sez. Chimica Generale e Organica "A. Marchesini" , Universitá degli Studi di Milano , via Venezian 21 , 20133 Milano , Italy .
| | - J Kaffy
- Molécules Fluorées et Chimie Médicinale , BioCIS , Univ. Paris-Sud , CNRS , Université Paris Saclay , 5 rue Jean-Baptiste Clément , 92296 Châtenay-Malabry Cedex , France .
| | - M Taverna
- Protéines et Nanotechnologies en Sciences Séparatives , Institut Galien Paris-Sud , Univ. Paris-Sud , CNRS , Université Paris Saclay , 5 rue Jean-Baptiste Clément , 92296 Châtenay-Malabry Cedex , France
| | - A Contini
- DISFARM-Sez. Chimica Generale e Organica "A. Marchesini" , Universitá degli Studi di Milano , via Venezian 21 , 20133 Milano , Italy .
| | - M Taylor
- Lancaster University , Division of Biomedical and Life Sciences , Faculty of Health and Medicine , Lancaster LA1 4YQ , UK
| | - D Allsop
- Lancaster University , Division of Biomedical and Life Sciences , Faculty of Health and Medicine , Lancaster LA1 4YQ , UK
| | - M L Gelmi
- DISFARM-Sez. Chimica Generale e Organica "A. Marchesini" , Universitá degli Studi di Milano , via Venezian 21 , 20133 Milano , Italy .
| | - S Ongeri
- Molécules Fluorées et Chimie Médicinale , BioCIS , Univ. Paris-Sud , CNRS , Université Paris Saclay , 5 rue Jean-Baptiste Clément , 92296 Châtenay-Malabry Cedex , France .
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4
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Kirubakaran P, Pfeiferová L, Boušová K, Bednarova L, Obšilová V, Vondrášek J. Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins. Proteins 2016; 84:1358-74. [DOI: 10.1002/prot.25082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Palani Kirubakaran
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Lucie Pfeiferová
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Kristýna Boušová
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
- Institute of Physiology ASCR; v.v.i, Videnska 1083, 14220 Prague 4 Czech Republic
| | - Lucie Bednarova
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Veronika Obšilová
- Institute of Physiology ASCR; v.v.i, Videnska 1083, 14220 Prague 4 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
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5
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Olajos G, Hetényi A, Wéber E, Németh LJ, Szakonyi Z, Fülöp F, Martinek TA. Induced folding of protein-sized foldameric β-sandwich models with core β-amino acid residues. Chemistry 2015; 21:6173-80. [PMID: 25677195 DOI: 10.1002/chem.201405581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 01/27/2023]
Abstract
The mimicry of protein-sized β-sheet structures with unnatural peptidic sequences (foldamers) is a considerable challenge. In this work, the de novo designed betabellin-14 β-sheet has been used as a template, and α→β residue mutations were carried out in the hydrophobic core (positions 12 and 19). β-Residues with diverse structural properties were utilized: Homologous β(3) -amino acids, (1R,2S)-2-aminocyclopentanecarboxylic acid (ACPC), (1R,2S)-2-aminocyclohexanecarboxylic acid (ACHC), (1R,2S)-2-aminocyclohex-3-enecarboxylic acid (ACEC), and (1S,2S,3R,5S)-2-amino-6,6-dimethylbicyclo[3.1.1]heptane-3-carboxylic acid (ABHC). Six α/β-peptidic chains were constructed in both monomeric and disulfide-linked dimeric forms. Structural studies based on circular dichroism spectroscopy, the analysis of NMR chemical shifts, and molecular dynamics simulations revealed that dimerization induced β-sheet formation in the 64-residue foldameric systems. Core replacement with (1R,2S)-ACHC was found to be unique among the β-amino acid building blocks studied because it was simultaneously able to maintain the interstrand hydrogen-bonding network and to fit sterically into the hydrophobic interior of the β-sandwich. The novel β-sandwich model containing 25 % unnatural building blocks afforded protein-like thermal denaturation behavior.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, 6720 Szeged (Hungary)
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6
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Schuchardt BJ, Mikles DC, Hoang LM, Bhat V, McDonald CB, Sudol M, Farooq A. Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity. FEBS J 2014; 281:5532-51. [PMID: 25283809 DOI: 10.1111/febs.13095] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/17/2014] [Accepted: 09/30/2014] [Indexed: 11/30/2022]
Abstract
YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules.
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Affiliation(s)
- Brett J Schuchardt
- Department of Biochemistry and Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
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7
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Cabrele C, Martinek TA, Reiser O, Berlicki Ł. Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry. J Med Chem 2014; 57:9718-39. [DOI: 10.1021/jm5010896] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chiara Cabrele
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Tamás A. Martinek
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6., H-6720 Szeged, Hungary
| | - Oliver Reiser
- Institute
of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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8
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Oxidation and Structural Modification of Full-Fat and Defatted Flour Based Soy Protein Isolates Induced by Natural and Synthetic Extraction Chemicals. FOOD BIOPHYS 2014. [DOI: 10.1007/s11483-014-9333-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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10
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Proline-glutamate chimera’s side chain conformation directs the type of β-hairpin structure. Amino Acids 2013; 46:177-86. [DOI: 10.1007/s00726-013-1610-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/19/2013] [Indexed: 01/02/2023]
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11
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Hegedüs Z, Wéber E, Kriston-Pál É, Makra I, Czibula Á, Monostori É, Martinek TA. Foldameric α/β-peptide analogs of the β-sheet-forming antiangiogenic anginex: structure and bioactivity. J Am Chem Soc 2013; 135:16578-84. [PMID: 24088182 DOI: 10.1021/ja408054f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The principles of β-sheet folding and design for α-peptidic sequences are well established, while those for sheet mimetics containing homologated amino acid building blocks are still under investigation. To reveal the structure-function relations of β-amino-acid-containing foldamers, we followed a top-down approach to study a series of α/β-peptidic analogs of anginex, a β-sheet-forming antiangiogenic peptide. Eight anginex analogs were developed by systematic α → β(3) substitutions and analyzed by using NMR and CD spectroscopy. The foldamers retained the β-sheet tendency, though with a decreased folding propensity. β-Sheet formation could be induced by a micellar environment, similarly to that of the parent peptide. The destructuring effect was higher when the α → β(3) exchange was located in the β-sheet core. Analysis of the β-sheet stability versus substitution pattern and the local conformational bias of the bulky β(3)V and β(3)I residues revealed that a mismatch between the H-bonding preferences of the α- and β-residues played a minor role in the structure-breaking effect. Temperature-dependent CD and NMR measurements showed that the hydrophobic stabilization was scaled-down for the α/β-peptides. Analysis of the biological activity of the foldamer peptides showed that four anginex derivatives dose-dependently inhibited the proliferation of a mouse endothelial cell line. The α → β(3) substitution strategy applied in this work can be a useful approach to the construction of bioactive β-sheet mimetics with a reduced aggregation tendency and improved pharmacokinetic properties.
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Affiliation(s)
- Zsófia Hegedüs
- SZTE-MTA Lendulet Foldamer Research Group, Institute of Pharmaceutical Chemistry, University of Szeged , Eötvös u. 6, H-6720 Szeged, Hungary
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12
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McDonald CB, Buffa L, Bar-Mag T, Salah Z, Bhat V, Mikles DC, Deegan BJ, Seldeen KL, Malhotra A, Sudol M, Aqeilan RI, Nawaz Z, Farooq A. Biophysical basis of the binding of WWOX tumor suppressor to WBP1 and WBP2 adaptors. J Mol Biol 2012; 422:58-74. [PMID: 22634283 DOI: 10.1016/j.jmb.2012.05.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/07/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022]
Abstract
The WW-containing oxidoreductase (WWOX) tumor suppressor participates in a diverse array of cellular activities by virtue of its ability to recognize WW-binding protein 1 (WBP1) and WW-binding protein 2 (WBP2) signaling adaptors among a wide variety of other ligands. Herein, using a multitude of biophysical techniques, we provide evidence that while the WW1 domain of WWOX binds to PPXY motifs within WBP1 and WBP2 in a physiologically relevant manner, the WW2 domain exhibits no affinity toward any of these PPXY motifs. Importantly, our data suggest that while R25/W44 residues located within the binding pocket of a triple-stranded β-fold of WW1 domain are critical for the recognition of PPXY ligands, they are replaced by the chemically distinct E66/Y85 duo at structurally equivalent positions within the WW2 domain, thereby accounting for its failure to bind PPXY ligands. Predictably, not only does the introduction of E66R/Y85W double substitution within the WW2 domain result in gain of function but the resulting engineered domain, hereinafter referred to as WW2_RW, also appears to be a much stronger binding partner of WBP1 and WBP2 than the wild-type WW1 domain. We also show that while the WW1 domain is structurally disordered and folds upon ligand binding, the WW2 domain not only adopts a fully structured conformation but also aids stabilization and ligand binding to WW1 domain. This salient observation implies that the WW2 domain likely serves as a chaperone to augment the physiological function of WW1 domain within WWOX. Collectively, our study lays the groundwork for understanding the molecular basis of a key protein-protein interaction pertinent to human health and disease.
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Affiliation(s)
- Caleb B McDonald
- Department of Biochemistry and Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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13
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Celis S, Gorrea E, Nolis P, Illa O, Ortuño RM. Designing hybrid foldamers: the effect on the peptide conformational bias of β- versus α- and γ-linear residues in alternation with (1R,2S)-2-aminocyclobutane-1-carboxylic acid. Org Biomol Chem 2012; 10:861-8. [DOI: 10.1039/c1ob06575k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Stewart AL, Park JH, Waters ML. Redesign of a WW domain peptide for selective recognition of single-stranded DNA. Biochemistry 2011; 50:2575-84. [PMID: 21332166 DOI: 10.1021/bi101116a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A β-sheet miniprotein based on the FBP11 WW1 domain sequence has been redesigned for the molecular recognition of ssDNA. A previous report showed that a β-hairpin peptide dimer, (WKWK)(2), binds ssDNA with low micromolar affinity but with little selectivity over duplex DNA. This report extends those studies to a three-stranded β-sheet miniprotein designed to mimic the OB-fold. The new peptide binds ssDNA with low micromolar affinity and shows about 10-fold selectivity for ssDNA over duplex DNA. The redesigned peptide no longer binds its native ligand, the polyproline helix, confirming that the peptide has been redesigned for the function of binding ssDNA. Structural studies provide evidence that this peptide consists of a well-structured β-hairpin made of strands 2 and 3 with a less structured first strand that provides affinity for ssDNA but does not improve the stability of the full peptide. These studies provide insight into protein-DNA interactions as well as a novel example of protein redesign.
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Affiliation(s)
- Amanda L Stewart
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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15
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Abstract
UDP-N-acetylglucosamine 3-O-acyltransferase is a protein with a left-handed parallel beta-helix, which is a natural nanotube. They are associated with unusual high stability. To identify the reason behind the structural stability of beta-helical nanotubular structure, we have performed a total of 4 mus molecular dynamics simulations of the protein in implicit solvent at four different temperatures and monitored the unfolding pathway. The correlation in movement between different regions of the nanotubular structure has been identified from the dynamical cross-correlation map and contribution of some specific residues towards unfolding transition has been identified by principal component analysis. Difference in stability of the three loop regions has also been characterized. Construction of the unfolding conformational energy landscape identifies the probable intermediates that can appear in the unfolding pathway of the protein.
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Affiliation(s)
- Atanu Das
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India
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16
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Tapia VE, Nicolaescu E, McDonald CB, Musi V, Oka T, Inayoshi Y, Satteson AC, Mazack V, Humbert J, Gaffney CJ, Beullens M, Schwartz CE, Landgraf C, Volkmer R, Pastore A, Farooq A, Bollen M, Sudol M. Y65C missense mutation in the WW domain of the Golabi-Ito-Hall syndrome protein PQBP1 affects its binding activity and deregulates pre-mRNA splicing. J Biol Chem 2010; 285:19391-401. [PMID: 20410308 DOI: 10.1074/jbc.m109.084525] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PQBP1 (polyglutamine tract-binding protein 1) gene encodes a nuclear protein that regulates pre-mRNA splicing and transcription. Mutations in the PQBP1 gene were reported in several X chromosome-linked mental retardation disorders including Golabi-Ito-Hall syndrome. The missense mutation that causes this syndrome is unique among other PQBP1 mutations reported to date because it maps within a functional domain of PQBP1, known as the WW domain. The mutation substitutes tyrosine 65 with cysteine and is located within the conserved core of aromatic amino acids of the domain. We show here that the binding property of the Y65C-mutated WW domain and the full-length mutant protein toward its cognate proline-rich ligands was diminished. Furthermore, in Golabi-Ito-Hall-derived lymphoblasts we showed that the complex between PQBP1-Y65C and WBP11 (WW domain-binding protein 11) splicing factor was compromised. In these cells a substantial decrease in pre-mRNA splicing efficiency was detected. Our study points to the critical role of the WW domain in the function of the PQBP1 protein and provides an insight into the molecular mechanism that underlies the X chromosome-linked mental retardation entities classified globally as Renpenning syndrome.
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Affiliation(s)
- Victor E Tapia
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin 10115, Germany
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17
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Weikl TR. Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins. Biophys J 2007; 94:929-37. [PMID: 17905840 PMCID: PMC2186242 DOI: 10.1529/biophysj.107.109868] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Phi-values for two small beta-sheet proteins, the PIN and the FBP WW domains. The native structure of these WW domains comprises two beta-hairpins that form a three-stranded beta-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in molecular dynamics folding-unfolding simulations of a small designed three-stranded beta-sheet protein. We obtain good agreement with the experimental data 1), by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins; and 2), by fitting a single parameter, the relative degree to which hairpins 1 and 2 are formed in the transition state. The model helps us to understand how mutations affect the folding kinetics of WW domains, and captures also negative Phi-values that have been difficult to interpret.
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Affiliation(s)
- Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany.
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