1
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Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024; 19:1583-1592. [PMID: 38916527 PMCID: PMC11299430 DOI: 10.1021/acschembio.4c00236] [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] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Alexis D. Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Stéphane P. Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
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2
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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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3
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Richaud AD, Mandal S, Das A, Roche SP. Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides. ACS Chem Biol 2023; 18:2555-2563. [PMID: 37976523 DOI: 10.1021/acschembio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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4
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Moxam J, Naylon S, Richaud AD, Zhao G, Padilla A, Roche SP. Passive Membrane Permeability of Sizable Acyclic β-Hairpin Peptides. ACS Med Chem Lett 2023; 14:278-284. [PMID: 36923919 PMCID: PMC10009788 DOI: 10.1021/acsmedchemlett.2c00486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The recent shift toward increasingly larger drug modalities has created a significant demand for novel classes of compounds with high membrane permeability that can inhibit intracellular protein-protein interactions (PPIs). While major advances have been made in the design of cell-permeable helices, stapled β-sheets, and cyclic peptides, the development of large acyclic β-hairpins lags far behind. Therefore, we investigated a series of 26 β-hairpins (MW > 1.6 kDa) belonging to a chemical space far beyond the Lipinski "rule of five" (fbRo5) and showed that, in addition to their innate plasticity, the lipophilicity of these peptides (log D 7.4 ≈ 0 ± 0.7) can be tuned to drastically improve the balance between aqueous solubility and passive membrane permeability.
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Affiliation(s)
- Jillene Moxam
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Sarah Naylon
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alexis D. Richaud
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
| | - Alberto Padilla
- Department
of Natural Science, Keiser University, Fort Lauderdale, Florida 33309, United States
| | - Stéphane P. Roche
- Department
of Chemistry and Biochemistry, Florida Atlantic
University, Boca Raton, Florida 33431, United States
- Center
for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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5
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Richaud AD, Zaghouani M, Zhao G, Wangpaichitr M, Savaraj N, Roche SP. Exploiting the Innate Plasticity of the Programmed Cell Death-1 (PD1) Receptor to Design Pembrolizumab H3 Loop Mimics. Chembiochem 2022; 23:e202200449. [PMID: 36082509 PMCID: PMC10029098 DOI: 10.1002/cbic.202200449] [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: 08/03/2022] [Revised: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Checkpoint blockade of the immunoreceptor programmed cell death-1 (PD1) with its ligand-1 (PDL1) by monoclonal antibodies such as pembrolizumab provided compelling clinical results in various cancer types, yet the molecular mechanism by which this drug blocks the PD1/PDL1 interface remains unclear. To address this question, we examined the conformational motion of PD1 associated with the binding of pembrolizumab. Our results revealed that the innate plasticity of both C'D and FG loops is crucial to form a deep binding groove (371 Å3 ) across several distant epitopes of PD1. This analysis ultimately provided a rational-design to create pembrolizumab H3 loop mimics [RDYRFDMGFD] into β-hairpin scaffolds. As a result, a 20-residue long β-hairpin peptide 1 e was identified as a first-in-class potent PD1-inhibitor (EC50 of 0.29 μM; Ki of 41 nM).
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mehdi Zaghouani
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | | | - Niramol Savaraj
- Miller School of Medicine, University of Miami, Miami, FL 33458, USA
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, FL 33458, USA
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6
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Hetényi A, Szabó E, Imre N, Bhaumik KN, Tököli A, Füzesi T, Hollandi R, Horvath P, Czibula Á, Monostori É, Deli MA, Martinek TA. α/β-Peptides as Nanomolar Triggers of Lipid Raft-Mediated Endocytosis through GM1 Ganglioside Recognition. Pharmaceutics 2022; 14:pharmaceutics14030580. [PMID: 35335956 PMCID: PMC8953856 DOI: 10.3390/pharmaceutics14030580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
Cell delivery of therapeutic macromolecules and nanoparticles is a critical drug development challenge. Translocation through lipid raft-mediated endocytic mechanisms is being sought, as it can avoid rapid lysosomal degradation. Here, we present a set of short α/β-peptide tags with high affinity to the lipid raft-associated ganglioside GM1. These sequences induce effective internalization of the attached immunoglobulin cargo. The structural requirements of the GM1-peptide interaction are presented, and the importance of the membrane components are shown. The results contribute to the development of a receptor-based cell delivery platform.
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Affiliation(s)
- Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
| | - Enikő Szabó
- Institute of Genetics, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary; (E.S.); (É.M.)
| | - Norbert Imre
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
| | - Kaushik Nath Bhaumik
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
| | - Attila Tököli
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
| | - Tamás Füzesi
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
| | - Réka Hollandi
- Institute of Biophysics, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary; (R.H.); (P.H.)
| | - Peter Horvath
- Institute of Biophysics, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary; (R.H.); (P.H.)
| | - Ágnes Czibula
- Institute of Genetics, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary; (E.S.); (É.M.)
- Correspondence: (Á.C.); (T.A.M.)
| | - Éva Monostori
- Institute of Genetics, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary; (E.S.); (É.M.)
| | - Mária A. Deli
- Synthetic and Systems Biology Unit, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary;
| | - Tamás A. Martinek
- Department of Medical Chemistry, University of Szeged, Dóm Tér 8, 6720 Szeged, Hungary; (A.H.); (N.I.); (K.N.B.); (A.T.); (T.F.)
- Correspondence: (Á.C.); (T.A.M.)
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7
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Abstract
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His3-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pKa of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
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8
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Solemanifar A, Guo X, Donose BC, Bertling K, Laycock B, Rakić AD. Probing peptide nanowire conductivity by THz nanoscopy. NANOTECHNOLOGY 2021; 33:065503. [PMID: 34715680 DOI: 10.1088/1361-6528/ac34a6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Significant efforts have recently been invested in assessing the physical and chemical properties of microbial nanowires for their promising role in developing alternative renewable sources of electricity, bioelectronic materials and implantable sensors. One of their outstanding properties, the ever-desirable conductivity has been the focus of numerous studies. However, the lack of a straightforward and reliable method for measuring it seems to be responsible for the broad variability of the reported data. Routinely employed methods tend to underestimate or overestimate conductivity by several orders of magnitude. In this work, synthetic peptide nanowires conductivity is interrogated employing a non-destructive measurement technique developed on a terahertz scanning near-field microscope to test if peptide aromaticity leads to higher electrical conductivity. Our novel peptide conductivity measurement technique, based on triple standards calibration method, shows that in the case of two biopolymer mimicking peptides, the sample incorporating aromatic residues (W6) is about six times more conductive than the negative control (L6). To the best of our knowledge, this is the first report of a quantitative nano-scale terahertz s-SNOM investigation of peptides. These results prove the suitability of the terahertz radiation-based non-destructive approach in tandem with the designer peptides choice as model test subjects. This approach requires only simple sample preparation, avoids many of the pitfalls of typical contact-based conductivity measurement techniques and could help understanding fundamental aspects of nature's design of electron transfer in biopolymers.
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Affiliation(s)
- Armin Solemanifar
- School of Chemical Engineering, The University of Queensland, QLD 4072, Australia
| | - Xiao Guo
- School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
| | - Bogdan C Donose
- School of Chemical Engineering, The University of Queensland, QLD 4072, Australia
- School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
| | - Karl Bertling
- School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
| | - Bronwyn Laycock
- School of Chemical Engineering, The University of Queensland, QLD 4072, Australia
| | - Aleksandar D Rakić
- School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
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9
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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10
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Sivanesam K, Kier BL, Whedon SD, Chatterjee C, Andersen NH. Biological consequences of improving the structural stability of hairpins that have antimicrobial activity. J Pept Sci 2018; 23:899-906. [PMID: 29193517 DOI: 10.1002/psc.3054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 11/11/2022]
Abstract
Designing new antimicrobial peptides (AMPs) focuses heavily on the activity of the peptide and less on the elements that stabilize the secondary structure of these peptides. Studies have shown that improving the structure of naturally occurring AMPs can affect activity and so here we explore the relationship between structure and activity of two non-naturally occurring AMPs. We have used a backbone-cyclized peptide as a template and designed an uncyclized analogue of this peptide that has antimicrobial activity. We focused on beta-hairpin-like structuring features. Improvements to the structure of this peptide reduced the activity of the peptide against gram-negative, Escherichia coli but improved the activity against gram-positive, Corynebacterium glutamicum. Distinctions in structuring effects on gram-negative versus gram-positive activity were also seen in a second peptide system. Structural improvements resulted in a peptide that was more active than the native against gram-positive bacterium but less active against gram-negative bacterium. Our results show that there is not always a correlation between improved hairpin-structuring and activity. Other factors such as the type of bacteria being targeted as well as net positive charge can play a role in the potency of AMPs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Kalkena Sivanesam
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Samuel D Whedon
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
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11
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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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12
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Anderson JM, Andersen NH. A pH Switch for β-Sheet Protein Folding. Angew Chem Int Ed Engl 2017; 56:7074-7077. [PMID: 28523654 PMCID: PMC5607017 DOI: 10.1002/anie.201700860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/26/2017] [Indexed: 01/24/2023]
Abstract
Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6-residue sequence (HPATGK) that acts as a stable structure-nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β-sheet, this leads to a pH switch of folding. Using a standard 3-stranded β-sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (Tm ) was observed at pH 2.5: ΔΔGF ≥11.3 kJ mol-1 . Using the strategies demonstrated in this article, the redesign of β-sheets to contain a global, or local, pH-dependent conformational switch should be possible.
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13
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A pH Switch for β-Sheet Protein Folding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Anderson JM, Shcherbakov AA, Kier BL, Kellock J, Shu I, Byrne AL, Eidenschink LA, Andersen NH. Optimization of a β-sheet-cap for long loop closure. Biopolymers 2017; 107. [PMID: 27701729 DOI: 10.1002/bip.22995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/25/2022]
Abstract
Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable β-sheet structures, including features that allow us to probe these questions. Using paired Trp residues that form aromatic clusters on folding, we are able to stabilize two β-strands connected by varying loop lengths and composition (an example sequence: RWITVTI - loop - KKIRVWE). Using NMR and CD, both fold stability and folding dynamics can be investigated for these systems. With the 16 residue loop peptide (sequence: RWITVTI-(GGGGKK)2 GGGG-KKIRVWE) remaining folded (ΔGU = 1.6 kJ/mol at 295K). To increase stability and extend the series to longer loops, we added an additional Trp/Trp pair in the loop flanking position. With this addition to the strands, the 16 residue loop (sequence: RWITVRIW-(GGGGKK)2 GGGG-WKTIRVWE) supports a remarkably stable β-sheet (ΔGU = 6.3 kJ/mol at 295 K, Tm = ∼55°C). Given the abundance of loops in binding motifs and between secondary structures, these constructs can be powerful tools for peptide chemists to study loop effects; with the Trp/Trp pair providing spectroscopic probes for assessing both stability and dynamics by NMR.
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Affiliation(s)
- Jordan M Anderson
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Jackson Kellock
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Aimee L Byrne
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington
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15
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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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16
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Anderson JM, Jurban B, Huggins KNL, Shcherbakov AA, Shu I, Kier B, Andersen NH. Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability. Biochemistry 2016; 55:5537-5553. [DOI: 10.1021/acs.biochem.6b00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jordan M. Anderson
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Kelly N. L. Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | | | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brandon Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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17
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Mukherjee D, Gai F. Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins. Anal Biochem 2016; 507:74-8. [PMID: 27251434 DOI: 10.1016/j.ab.2016.05.017] [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: 03/31/2016] [Revised: 05/14/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022]
Abstract
Exciton coupling between two chromophores can produce a circular dichroism (CD) couplet that depends on their separation distance, among other factors. Therefore, exciton CD signals arising from aromatic sidechains, especially those of tryptophan (Trp), have been used in various protein conformational studies. However, the long-wavelength component of the commonly used CD couplet produced by a pair of Trp residues is typically located around 230 nm, thereby overlapping significantly with the protein backbone CD signal. This overlap often prevents a direct and quantitative assessment of the Trp CD couplet in question without further spectral analysis. Here, we show that this inconvenience can be alleviated by using a derivative of Trp, 5-cyanotryptophan (TrpCN), as the chromophore. Specifically, through studying a series of peptides that fold into either α-helical or ß-hairpin conformations, we demonstrate that in comparison with the Trp CD couplet, that arising from two TrpCN residues not only is significantly red-shifted but also becomes more intense due to the larger extinction coefficient of the underlying electronic transition. In addition, we show that a pair of p-cyanophenylalanines (PheCN) or a PheCN-TrpCN pair can also produce a distinct exciton CD couplet that can be useful in monitoring conformational changes in proteins.
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Affiliation(s)
- Debopreeti Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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