1
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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [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: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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2
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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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3
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Victorio CG, Sawyer N. Folding-Assisted Peptide Disulfide Formation and Dimerization. ACS Chem Biol 2023; 18:1480-1486. [PMID: 37390465 DOI: 10.1021/acschembio.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Disulfide bonds form covalent bonds between distal regions of peptides and proteins to dramatically impact their folding, stability, and oligomerization. Given the prevalence of disulfide bonds in many natural products, considerable effort has been invested in site-selective disulfide bond formation approaches to control the folding of chemically synthesized peptides and proteins. Here, we show that the careful choice of thiol oxidation conditions can lead to monomeric or dimeric species from fully deprotected linear bisthiol peptides. Starting from a p53-derived peptide, we found that oxidation under aqueous (nondenaturing) conditions produces antiparallel dimers with enhanced α-helical character, while oxidation under denaturing conditions promotes formation of a nonhelical intramolecular disulfide species. Examination across peptide variants suggests that intramolecular disulfide formation is robust across diverse peptide sequences, while dimerization is sensitive to both the α-helical folding of the linear peptide and aromatic residues at the dimerization interface. All disulfide species are more resistant to protease degradation than the linear peptide but are easily reduced to restore the initial bisthiol peptide. Both disulfide formation approaches are compatible with α-helix-stabilizing cross-linkers. These results provide an approach for using disulfide bonds to control peptide folding and oligomerization to better understand how folding influences interactions with diverse molecular targets.
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Affiliation(s)
- Clara G Victorio
- Department of Chemistry, Fordham University, 441 E. Fordham Rd., Bronx, New York 10458, United States
| | - Nicholas Sawyer
- Department of Chemistry, Fordham University, 441 E. Fordham Rd., Bronx, New York 10458, United States
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4
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Tram NDT, Selvarajan V, Boags A, Mukherjee D, Marzinek JK, Cheng B, Jiang ZC, Goh P, Koh JJ, Teo JWP, Bond PJ, Ee PLR. Manipulating turn residues on de novo designed β-hairpin peptides for selectivity against drug-resistant bacteria. Acta Biomater 2021; 135:214-224. [PMID: 34506975 DOI: 10.1016/j.actbio.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/19/2022]
Abstract
Synthetic β-hairpin antimicrobial peptides (AMPs) offer a useful source for the development of novel antimicrobial agents. β-hairpin peptides generally consist of two side strands bridged by a reverse turn. In literature, most studies focused on the modifications of the side strands to manipulate the stability and activity of β-hairpin peptides, and much less is known about the impact of the turn region. By designing a series of de novo β-hairpin peptides with identical side strands but varied turns, we demonstrated that mutations of only 2 to 4 amino acids at the turn region could impart a wide range of antimicrobial profiles among synthetic β-hairpin AMPs. BTT2-4 and BTT6 displayed selective potency against Gram-negative bacteria, with minimum inhibitory concentrations (MICs) of 4-8 µM. In contrast, BTT1 exhibited broad-spectrum activity, with MICs of 4-8 µM against both Gram-positive and Gram-negative strains. Additionally, BTT1 was potent against methicillin-resistant Staphylococcus aureus (MRSA) and colistin-resistant Enterobacterales. The antimicrobial potency of BTT1 persisted after 14 days of serial passage. Mechanistic studies revealed that interactions between lipopolysaccharide (LPS) and the peptides were critical to their membranolytic activity against the bacterial inner membrane. Aside from folding stability, we observed that a degree of conformational flexibility was required for disruptive membrane interactions. STATEMENT OF SIGNIFICANCE: By examining the significance of the turn region of β-hairpin peptides, we present valuable knowledge to the design toolkit of novel antimicrobial peptides as alternative therapeutics to overcome antibiotic resistance. Our de novo designed synthetic peptides displayed selective activity against Gram-negative bacteria and potent activity against clinically relevant antibiotic-resistant strains (e.g. colistin-resistant Enterobacterales and methicillin-resistant Staphylococcus aureus). The bactericidal activity of our peptides was shown to be robust in the presence of proteolytic trypsin and saline, conditions that could suppress peptide activity. Our peptides were also determined to be non-cytotoxic against a human cell line.
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Affiliation(s)
- Nhan D T Tram
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore
| | - Vanitha Selvarajan
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore
| | - Alister Boags
- Bioinformatics Institute, Agency of Science, Technology and Research (A*STAR), 138671, Singapore, Singapore; School of Chemistry, University of Southampton, SO17 1BJ, Southampton, United Kingdom
| | - Devika Mukherjee
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute, Agency of Science, Technology and Research (A*STAR), 138671, Singapore, Singapore
| | - Bernadette Cheng
- Department of Laboratory Medicine, Microbiology Unit, National University Hospital, 119074, Singapore , Singapore
| | - Zi-Chen Jiang
- Department of Pharmacology and Toxicology, University of Toronto, M5S 1A1, Ontario, Canada
| | - Pascal Goh
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore
| | - Jun-Jie Koh
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, Microbiology Unit, National University Hospital, 119074, Singapore , Singapore
| | - Peter J Bond
- Bioinformatics Institute, Agency of Science, Technology and Research (A*STAR), 138671, Singapore, Singapore; National University of Singapore, Department of Biological Sciences, 117558, Singapore, Singapore
| | - Pui Lai Rachel Ee
- Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, 119077, Singapore, Singapore.
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5
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Lella M, Mahalakshmi R. De novo
design of metal‐binding cleft in a
Trp‐Trp
stapled thermostable β‐hairpin peptide. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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6
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Wendt M, Bellavita R, Gerber A, Efrém NL, van Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez-Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021; 60:13937-13944. [PMID: 33783110 PMCID: PMC8252567 DOI: 10.1002/anie.202102082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.
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Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nina-Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Thirza van Ramshorst
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicholas M Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Paul R J Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Isabel Everard
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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7
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Wendt M, Bellavita R, Gerber A, Efrém N, Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez‐Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β‐Sheet Mimetics that Target the Transcriptional Coactivator β‐Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nina‐Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Thirza Ramshorst
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | | | - Isabel Everard
- Mechanistic Biology and Profiling Discovery Sciences, R&D AstraZeneca Cambridge UK
| | | | | | - Paolo Grieco
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
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8
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Di Natale C, La Manna S, Avitabile C, Florio D, Morelli G, Netti PA, Marasco D. Engineered β-hairpin scaffolds from human prion protein regions: Structural and functional investigations of aggregates. Bioorg Chem 2020; 96:103594. [PMID: 31991323 DOI: 10.1016/j.bioorg.2020.103594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/16/2022]
Abstract
The investigation of conformational features of regions of amyloidogenic proteins are of great interest to deepen the structural changes and consequent self-aggregation mechanisms at the basis of many neurodegenerative diseases. Here we explore the effect of β-hairpin inducing motifs on regions of prion protein covering strands S1 and S2. In detail, we unveiled the structural and functional features of two model chimeric peptides in which natural sequences are covalently linked together by two dipeptides (l-Pro-Gly and d-Pro-Gly) that are known to differently enhance β-hairpin conformations but both containing N- and the C-terminal aromatic cap motifs to further improve interactions between natural strands. Spectroscopic investigations at solution state indicate that primary assemblies of the monomers of both constructs follow different aggregativemechanisms during the self-assembly: these distinctions, evidenced by CD and ThT emission spectroscopies, reflect into great morphological differences of nanostructures and suggest that rigid β-hairpin conformations greatly limit amyloid-like fibrillogenesis. Overall data confirm the important role exerted by the β-structure of regions S1 and S2 during the aggregation process and lead to speculate to its persistence even in unfolding conditions.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Task force di Ateneo"METODOLOGIE ANALITICHE PER LA SALVAGUARDIA DEI BENI CULTURALI" MASBC, University of Naples "Federico II", Italy.
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9
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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10
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Dong H, Meng X, Zheng X, Cheng X, Zheng Y, Zhao Y, Wu C. Design and Synthesis of Cross-Link-Dense Peptides by Manipulating Regioselective Bisthioether Cross-Linking and Orthogonal Disulfide Pairing. J Org Chem 2019; 84:5187-5194. [PMID: 30895794 DOI: 10.1021/acs.joc.9b00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Existing disulfide-rich peptides, both naturally occurring and de novo designed, only represent a tiny amount of the possible sequence space because natural evolution and de novo design only keep sequences that are structurally approachable by correct disulfide pairings. To bypass this limitation for designing new peptide scaffolds beyond the natural sequence space, we dedicate to developing novel disulfide-rich peptides with predefined disulfide pairing patterns irrelevant to primary sequences. However, most of these designed peptides still suffer from disulfide rearrangements to at least one to three possible isomers. Here, we report a general and reliable strategy for the design and synthesis of a range of structurally diverse cross-link-dense peptide (CDP) scaffolds with two orthogonal disulfide bonds and a bisthioether bridge that are not subject to disulfide isomerizations. Altering the pattern of cysteine and penicillamine generates hundreds of different CDP scaffolds tolerant to extensive sequence manipulations. This work thus provides many useful scaffolds for the design of functional molecules such as protein binders with improved proteolytic stability (e.g., designed by epitope grafting).
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Affiliation(s)
- Huilei Dong
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Xiaoting Meng
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Xiaoli Zheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Xueting Cheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Yiwu Zheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Yibing Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation , Xiamen University , Xiamen 361005 , P.R. China
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11
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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12
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Lahiri P, Verma H, Ravikumar A, Chatterjee J. Protein stabilization by tuning the steric restraint at the reverse turn. Chem Sci 2018; 9:4600-4609. [PMID: 29899953 PMCID: PMC5969505 DOI: 10.1039/c7sc05163h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
The incorporation of pseudoallylic strain by N-methylation at the solvent exposed loop in proteins leads to a stark increase in their thermodynamic stability that can be tuned by altering the amino acid composition.
Reverse turns are solvent-exposed motifs in proteins that are crucial in nucleating β-sheets and drive the protein folding. The solvent-exposed nature makes reverse turns more amenable to chemical modifications than α-helices or β-sheets towards modulating the stability of re-engineered proteins. Here, we utilize van der Waals repulsive forces in tuning the steric restraint at the reverse turn. The steric restraint induced upon N-methylation of the i+1–i+2 amide bond at the reverse turn results in well-folded and stable β-sheets in aqueous solution at room temperature. The developed superactive turn inducing motif is tolerant to a wide variety of functional groups present on coded amino acids making the designed turn fully compatible with bioactive loops in proteins. We demonstrate that the steric restraint and the functional groups at the reverse turn act in synergy to modulate the folding of re-engineered β-sheets. Introduction of the turn motifs onto a three-stranded β-sheet protein, Pin 1 WW domain, resulted in various analogs showing a cooperative two-state transition with thermal stability (TM) ranging from 62 °C to 82 °C. Despite modulating the stability of Pin 1 variants by ∼2.8 kcal mol–1 (ΔΔGf), the native fold in all the protein variants was found to be unperturbed. This structural stability is brought about by conformational preorganization at the engineered reverse turn that results in strong intramolecular hydrogen bonds along the three dimensional structure of the protein. Thus, this simple loop engineering strategy via two amino acid substitution provides us a “toolkit” to modulate the stability of β-sheet containing peptides and proteins in aqueous solution that will greatly expand the scope of de novo protein and foldamer design.
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Affiliation(s)
- Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Ashraya Ravikumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
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13
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Thomas NC, Bartlett GJ, Woolfson DN, Gellman SH. Toward a Soluble Model System for the Amyloid State. J Am Chem Soc 2017; 139:16434-16437. [PMID: 29116774 PMCID: PMC5939379 DOI: 10.1021/jacs.7b07225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The formation and deposition of amyloids is associated with many diseases. β-Sheet secondary structure is a common feature of amyloids, but the packing of sheets against one another is distinctive relative to soluble proteins. Standard methods that rely on perturbing a polypeptide's sequence and evaluating impact on folding can be problematic for amyloid aggregates because a single sequence can adopt multiple conformations and diverse packing arrangements. We describe initial steps toward a minimum-sized, soluble model system for the amyloid state that supports comparisons among sequence variants. Critical to this goal is development of a new linking strategy to enable intersheet association mediated by side chain interactions, which is characteristic of the amyloid state. The linker design we identified should ultimately support exploration of relationships between sequence and amyloid state stability for specific strand-association modes.
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Affiliation(s)
- Nicole C. Thomas
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Gail J. Bartlett
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1 TD, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Derek N. Woolfson
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1 TD, UK; BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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14
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Lin Y, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Sci 2017; 26:2187-2194. [PMID: 28801928 PMCID: PMC5654858 DOI: 10.1002/pro.3270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
We have previously shown that monomeric globular αβ-proteins can be designed de novo with considerable control over topology, size, and shape. In this paper, we investigate the design of cyclic homo-oligomers from these starting points. We experimented with both keeping the original monomer backbones fixed during the cyclic docking and design process, and allowing the backbone of the monomer to conform to that of adjacent subunits in the homo-oligomer. The latter flexible backbone protocol generated designs with shape complementarity approaching that of native homo-oligomers, but experimental characterization showed that the fixed backbone designs were more stable and less aggregation prone. Designed C2 oligomers with β-strand backbone interactions were structurally confirmed through x-ray crystallography and small-angle X-ray scattering (SAXS). In contrast, C3-C5 designed homo-oligomers with primarily nonpolar residues at interfaces all formed a range of oligomeric states. Taken together, our results suggest that for homo-oligomers formed from globular building blocks, improved structural specificity will be better achieved using monomers with increased shape complementarity and with more polar interfaces.
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Affiliation(s)
- Yu‐Ru Lin
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
| | - Nobuyasu Koga
- Research Center of Integrative Molecular SystemsInstitute for Molecular Science, National Institute of Natural Sciences (NINS)Okazaki 444‐8585Japan
- JST, PRESTOKawaguchiSaitama 332‐0012Japan
| | - Sergey M. Vorobiev
- Department of Biological ScienceNortheast Structural Genomics Consortium, Columbia UniversityNew YorkNew York
| | - David Baker
- Department of BiochemistryUniversity of Washington, and Howard Hughes Medical InstituteSeattleWashington 98195
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15
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Ge Y, Kier BL, Andersen NH, Voelz VA. Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models. J Chem Inf Model 2017; 57:1609-1620. [PMID: 28614661 DOI: 10.1021/acs.jcim.7b00132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular simulation has been used to model the detailed folding properties of peptides, yet prospective computational peptide design by such approaches remains challenging and nontrivial. To test the accuracy of simulation-based hairpin design, we characterized the folding properties of a series of so-called β-cap hairpin peptides designed to mimic a conserved hairpin of LapD, a bacterial intracellular signaling protein, both experimentally by NMR spectroscopy and computationally by implicit-solvent replica-exchange molecular dynamics using three different AMBER force fields (ff96, ff99sb-ildn, and ff99sb-ildn-NMR). A unique challenge presented by these designs is the presence of both a terminal Trp-Trp capping motif and a conserved GWxQ motif in the hairpin turn required for binding to LapG. Consistent with previous studies, we found AMBER ff96 to be the most accurate when used with the OBC GBSA implicit solvent model, despite its known bias toward β-sheet conformations when used in explicit-solvent simulations. To gain microscopic insight into the folding landscape of the hairpin designs, we additionally performed parallel simulations on the Folding@home distributed computing platform using AMBER ff99sb-ildn-NMR with TIP3P explicit solvent. Markov state models (MSMs) built from trajectory data reveal a number of non-native interactions between Trp and other amino acid side chains, creating potential problems in achieving well-folded hairpin structures in solution.
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Affiliation(s)
- Yunhui Ge
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Brandon L Kier
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Niels H Andersen
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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16
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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17
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Zheng L, Yu C, Zhan Y, Deng X, Wang Y, Jiang H. Locking Interconversion of Aromatic Oligoamide Foldamers by Intramolecular Side-chain Crosslinking: toward Absolute Control of Helicity in Synthetic Aromatic Foldamers. Chemistry 2017; 23:5361-5367. [DOI: 10.1002/chem.201700134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Lu Zheng
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Chengyuan Yu
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Yulin Zhan
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Xuebin Deng
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Ying Wang
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
| | - Hua Jiang
- Key Laboratory of Theoretical and Computational Photochemistry, and Key Laboratory of Radiopharmaceuticals; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 P. R. China
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18
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Sivanesam K, Kier BL, Whedon SD, Chatterjee C, Andersen NH. Hairpin structure stability plays a role in the activity of two antimicrobial peptides. FEBS Lett 2016; 590:4480-4488. [PMID: 27859052 DOI: 10.1002/1873-3468.12477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 11/06/2022]
Abstract
Many naturally occurring antimicrobial peptides (AMPs) are amphipathic with a β-hairpin conformation stabilized by cross-strand disulfides across the associated β-strands. Here, we show that the disulfides are not essential. Other structuring means such as better β-turns and noncovalent cross-strand interactions can, with proper design, replace the disulfides with no loss in antimicrobial activity. Our results also demonstrate that the hairpin turn region may play a role in membrane recognition for at least one member of this class, since a homodimeric turnless β-sheet analog showed no antimicrobial activity. We also examined the effects of N-terminal fatty acid adducts on AMPs. Surprisingly, the large hydrophobic carboxylic moieties examined completely eliminated the antimicrobial activity of previously active β-hairpin peptides.
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Affiliation(s)
| | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Samuel D Whedon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, USA
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19
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Cheung WL, Chen M, Maksimov MO, Link AJ. Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA. ACS CENTRAL SCIENCE 2016; 2:702-709. [PMID: 27800552 PMCID: PMC5084080 DOI: 10.1021/acscentsci.6b00184] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Lasso peptides are a member of the superclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Like all RiPPs, lasso peptides are derived from a gene-encoded precursor protein. The biosynthesis of lasso peptides requires two enzymatic activities: proteolytic cleavage between the leader peptide and the core peptide in the precursor protein, accomplished by the B enzymes, and ATP-dependent isopeptide bond formation, accomplished by the C enzymes. In a subset of lasso peptide biosynthetic gene clusters from Gram-positive organisms, the B enzyme is split between two proteins. One such gene cluster is found in the organism Rhodococcus jostii, which produces the antimicrobial lasso peptide lariatin. The B enzyme in R. jostii is split between two open reading frames, larB1 and larB2, both of which are required for lariatin biosynthesis. While the cysteine catalytic triad is found within the LarB2 protein, LarB1 is a PqqD homologue expected to bind to the lariatin precursor LarA based on its structural homology to other RiPP leader peptide binding domains. We show that LarB1 binds to the leader peptide of the lariatin precursor protein LarA with a sub-micromolar affinity. We used photocrosslinking with the noncanonical amino acid p-azidophenylalanine and mass spectrometry to map the interaction of LarA and LarB1. This analysis shows that the LarA leader peptide interacts with a conserved motif within LarB1 and, unexpectedly, the core peptide of LarA also binds to LarB1 in several positions. A Rosetta model built from distance restraints from the photocrosslinking experiments shows that the scissile bond between the leader peptide and core peptide in LarA is in a solvent-exposed loop.
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Affiliation(s)
- Wai Ling Cheung
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Maria
Y. Chen
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Mikhail O. Maksimov
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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20
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Craven TW, Bonneau R, Kirshenbaum K. PPII Helical Peptidomimetics Templated by Cation-π Interactions. Chembiochem 2016; 17:1824-1828. [PMID: 27539882 DOI: 10.1002/cbic.201600248] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 11/06/2022]
Abstract
Poly-proline type II (PPII) helical PXXP motifs are the recognition elements for a variety of protein-protein interactions that are critical for cellular signaling. Despite development of protocols for locking peptides into α-helical and β-strand conformations, there remains a lack of analogous methods for generating mimics of PPII helical structures. We describe herein a strategy to enforce PPII helical secondary structure in the 19-residue TrpPlexus miniature protein. Through sequence variation, we showed that a network of cation-π interactions could drive the formation of PPII helical conformations for both peptide and N-substituted glycine peptoid residues. The achievement of chemically diverse PPII helical scaffolds provides a new route towards discovering peptidomimetic inhibitors of protein-protein interactions mediated by PXXP motifs.
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Affiliation(s)
- Timothy W Craven
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.,Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY, 10003, USA
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY, 10003, USA.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA.,Simons Center for Data Analysis, 160 5th Ave., New York, NY, 10010, USA
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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21
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Kier BL, Newbloom GM, Pozzo LD, Andersen NH. A Structuring Repeat for Peptide Design: Long Beta Ribbons. Chembiochem 2016; 17:224-7. [PMID: 26603832 DOI: 10.1002/cbic.201500618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Beta sheets are inherently length-limited; adding residues to the ends of model β-sheets does not necessarily grow the β-sheet. Here, we present a method for extending β-sheets to any length with a stabilizing repeat unit containing cross-strand Trp residues. Beta ribbons as long as 35 residues (approaching 100 Å in length) are reported and characterized.
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Affiliation(s)
- Brandon L Kier
- Department of Chemistry, University of Washington, Box 351700, Bagley Hall, Seattle, WA, 98195-1700, USA.
| | - Gregory M Newbloom
- Department of Chemical Engineering, University of Washington, Box 351750, Benson Hall, Seattle, WA, 98195-1750, USA
| | - Lilo D Pozzo
- Department of Chemical Engineering, University of Washington, Box 351750, Benson Hall, Seattle, WA, 98195-1750, USA
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Box 351700, Bagley Hall, Seattle, WA, 98195-1700, USA.
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22
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Zheng Y, Zhai L, Zhao Y, Wu C. Orthogonal Cysteine–Penicillamine Disulfide Pairing for Directing the Oxidative Folding of Peptides. J Am Chem Soc 2015; 137:15094-7. [DOI: 10.1021/jacs.5b10779] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yiwu Zheng
- The MOE Key Laboratory of
Spectrochemical Analysis and Instrumentation, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Linxiang Zhai
- The MOE Key Laboratory of
Spectrochemical Analysis and Instrumentation, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yibing Zhao
- The MOE Key Laboratory of
Spectrochemical Analysis and Instrumentation, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Chuanliu Wu
- The MOE Key Laboratory of
Spectrochemical Analysis and Instrumentation, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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