51
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Riemen AJ, Waters ML. Dueling post-translational modifications trigger folding and unfolding of a beta-hairpin peptide. J Am Chem Soc 2010; 132:9007-13. [PMID: 20536234 DOI: 10.1021/ja101079z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein post-translational modifications (PTMs) are used in nature as a means of turning on or off a myriad of biological events. Methylation of lysine and phosphorylation of serine are important PTMs in the histone code found to modulate chromatin packing, which in turn affects gene expression. The design of peptides that fold into secondary structures can help to further our understanding of complex protein interactions. Here we report the design of the Trpswitch peptide sequence that folds into a moderately stable beta-hairpin structure in aqueous solution and show that the stability of the structure can be tuned by incorporation of dimethyllysine or phosphoserine. Dimethylated Trpswitch results in an increase in beta-hairpin stability, while phosphorylated Trpswitch is unstructured at neutral pH. When both modifications are incorporated into Trpswitch, a less stable beta-hairpin structure is observed. This system provides a model to demonstrate how multiple PTMs may work in concert or against each other to influence structure.
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Affiliation(s)
- Alexander J Riemen
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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52
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Yan Z, Wang J, Zhang J, Qin M, Wang W. Structural selection of ionic-complementary peptides with electrostatic interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:031917. [PMID: 21230118 DOI: 10.1103/physreve.82.031917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 06/21/2010] [Indexed: 05/30/2023]
Abstract
The structures of the peptides and their assembly are largely modulated by the environment. To discover the physical principles governing the structural modulations of peptides by the environment would be useful for many applications. As the typical examples, the structures of three kinds of ionic-complementary EAK16-family peptides under various environmental conditions are studied with simulations in this work. A model with intermediate resolution is used, in which both the backbone hydrogen bonds and electrostatic interactions are explicitly considered. The thermodynamics of these peptides (including the free energy and heat capacity) are described for various strengths of the electrostatic interactions which reflect the variation of environment. With these results, the phase diagrams of these peptides related to the temperature and the strength of electrostatic interactions are presented and compared. Based on the differences in the phase structures of the peptide, the different aggregation behaviors are explained based on the monomeric structural features of the peptides. Through the analysis on the stability of various secondary structures of these peptides, it is demonstrated that the charge pattern is the basic reason of the different responses of the EAK16-family peptides to the environmental changes. These results provide some examples and insights for the principles of structural selection by environment and may be helpful for further analysis and designs of peptide systems.
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Affiliation(s)
- Zhiqiang Yan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
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53
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Lin EI, Shell MS. Can Peptide Folding Simulations Provide Predictive Information for Aggregation Propensity? J Phys Chem B 2010; 114:11899-908. [DOI: 10.1021/jp104114n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edmund I. Lin
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080
| | - M. Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080
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54
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Banta S, Wheeldon IR, Blenner M. Protein Engineering in the Development of Functional Hydrogels. Annu Rev Biomed Eng 2010; 12:167-86. [PMID: 20420519 DOI: 10.1146/annurev-bioeng-070909-105334] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027;
| | - Ian R. Wheeldon
- Department of Chemical Engineering, Columbia University, New York, New York 10027;
| | - Mark Blenner
- Current address: Department of Medicine, Center for Biomedical Engineering, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115;
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55
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Nguyen TD, Glotzer SC. Reconfigurable assemblies of shape-changing nanorods. ACS NANO 2010; 4:2585-2594. [PMID: 20408583 DOI: 10.1021/nn901725b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Reconfigurable nanostructures represent an exciting new direction for materials. Applications of reversible transformations between nanostructures induced by molecular conformations under external fields can be found in a broad range of advanced technologies including smart materials, electromagnetic sensors, and drug delivery. With recent breakthroughs in synthesis and fabrication techniques, shape-changing nanoparticles are now possible. Such novel building blocks provide a conceptually new and exciting approach to self-assembly and phase transformations by providing tunable parameters fundamentally different from the usual thermodynamic parameters. Here we investigate via molecular simulation a transformation between two thermodynamically stable structures self-assembled by laterally tethered nanorods whose rod length is switched between two values. Building blocks with longer rods assemble into a square grid structure, while those with short rods form bilayer sheets with internal smectic A ordering at the same thermodynamic conditions. By shortening or lengthening the rods over a short time scale relative to the system equilibration time, we observe a transformation from the square grid structure into bilayer sheets, and vice versa. We also observe honeycomb grid and pentagonal grid structures for intermediate rod lengths. The reconfiguration between morphologically distinct nanostructures induced by dynamically switching the building block shape serves to motivate the fabrication of shape-changing nanoscale building blocks as a new approach to the self-assembly of reconfigurable materials.
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Affiliation(s)
- Trung Dac Nguyen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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56
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Blenner MA, Shur O, Szilvay GR, Cropek DM, Banta S. Calcium-induced folding of a beta roll motif requires C-terminal entropic stabilization. J Mol Biol 2010; 400:244-56. [PMID: 20438736 DOI: 10.1016/j.jmb.2010.04.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 11/30/2022]
Abstract
Beta roll motifs are associated with several proteins secreted by the type 1 secretion system (T1SS). Located just upstream of the C-terminal T1SS secretion signal, they are believed to act as calcium-induced switches that prevent folding before secretion. Bordetella pertussis adenylate cyclase (CyaA) toxin has five blocks of beta roll motifs (or repeats-in-toxin motifs) separated by linkers. The block V motif on its own has been reported to be non-responsive to calcium. Only when the N- and C-terminal linkers, or flanking groups, were fused did the motif bind calcium and fold. In an effort to understand the requirements for beta roll folding, we have truncated the N- and C-terminal flanks at several locations to determine the minimal essential sequences. Calcium-responsive beta roll folding occurred even in the absence of the natural N-terminal flank. The natural C-terminal flank could not be truncated without decreased calcium affinity and only partially truncated before losing calcium-responsiveness. Globular protein fusion at the C-terminus likewise enabled calcium-induced folding but fusions solely at the N-terminus failed. This demonstrates that calcium-induced folding is an inherent property of the beta roll motif rather than the flanking groups. Given the disparate nature of the observed functional flanking groups, C-terminal fusions appear to confer calcium-responsiveness to the beta roll motif via a non-specific mechanism, suggesting that entropic stabilization of the unstructured C-terminus can enable beta roll folding. Increased calcium affinity was observed when the natural C-terminal flank was used to enable calcium-induced folding, pointing to its cooperative participation in beta roll formation. This work indicates that a general principle of C-terminal entropic stabilization can enable stimulus-responsive repeat protein folding, while the C-terminal flank has a specific role in tuning calcium-responsive beta roll formation. These observations are in stark contrast to what has been reported for other repeat proteins.
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Affiliation(s)
- Mark A Blenner
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
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57
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Lu HD, Wheeldon IR, Banta S. Catalytic biomaterials: engineering organophosphate hydrolase to form self-assembling enzymatic hydrogels. Protein Eng Des Sel 2010; 23:559-66. [DOI: 10.1093/protein/gzq026] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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58
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Abstract
Chemical biology aims for a perfect control of protein complexes in time and space by their site-specific labeling, manipulation, and structured organization. Here we developed a self-inactivated, lock-and-key recognition element whose binding to His-tagged proteins can be triggered by light from zero to nanomolar affinity. Activation is achieved by photocleavage of a tethered intramolecular ligand arming a multivalent chelator head for high-affinity protein interaction. We demonstrate site-specific, stable, and reversible binding in solution as well as at interfaces controlled by light with high temporal and spatial resolution. Multiplexed organization of protein complexes is realized by an iterative in situ writing and binding process via laser scanning microscopy. This light-triggered molecular recognition should allow for a spatiotemporal control of protein-protein interactions and cellular processes by light-triggered protein clustering.
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59
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Guo Y, Xia F, Xu L, Li J, Yang W, Jiang L. Switchable wettability on cooperative dual-responsive poly-L-lysine surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1024-8. [PMID: 20030299 DOI: 10.1021/la9041452] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A cooperative dual-responsive polypeptide surface switching between superhydrophilic and superhydrophobic states is presented. This macroscopic phenomenon of surface originates from the combination of the cooperative unfolding/aggregation of the poly-L-lysine (PLL) immobilized on the substrate with micro/nanocomposite structure in response to pH and temperature. At pH lower than the pK(a) of PLL (approximately 11.0), PLL mainly adopts a random coil conformation, which corresponds to the superhydrophilic state on the rough surface substrate. Raising the pH to higher than the pK(a) allows the appearance of alpha-helix conformation, which also corresponds to the hydrophilic state. However, heating up the surface at pH higher than the pK(a) destabilizes the alpha-helix conformation and induces the formation of aggregated beta-sheet structures, which represents the superhydrophobic state. Lowering the pH and temperature simultaneously switches a reversible conversion from superhydrophobic to superhydrophilic states. In the switching process, the hydrophobicity and hydrophilicity can be "memorized" due to the cooperative pH and temperature stimuli-induced unfolding/aggregation behaviors of PLL. This provides a new exciting prospect for understanding surface properties of polypeptides and the design of smart material surfaces with potential applications in nanodevices, bioseparation, and biosensors.
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Affiliation(s)
- Yi Guo
- Key Laboratory of Surface and Interface Chemistry of Jilin Province, College of Chemistry, Jilin University, Changchun 130012, PR China
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60
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Löwik DWPM, Leunissen EHP, van den Heuvel M, Hansen MB, van Hest JCM. Stimulus responsive peptide based materials. Chem Soc Rev 2010; 39:3394-412. [DOI: 10.1039/b914342b] [Citation(s) in RCA: 248] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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61
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Szilvay GR, Blenner MA, Shur O, Cropek DM, Banta S. A FRET-based method for probing the conformational behavior of an intrinsically disordered repeat domain from Bordetella pertussis adenylate cyclase. Biochemistry 2009; 48:11273-82. [PMID: 19860484 DOI: 10.1021/bi901447j] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A better understanding of the conformational changes exhibited by intrinsically disordered proteins is necessary as we continue to unravel their myriad biological functions. In repeats in toxin (RTX) domains, calcium binding triggers the natively unstructured domain to adopt a beta roll structure. Here we present an in vitro Forster resonance energy transfer (FRET)-based method for the investigation of the conformational behavior of an RTX domain from the Bordetella pertussis adenylate cyclase consisting of nine repeat units. Equilibrium and stopped-flow FRET between fluorescent proteins, attached to the termini of the domain, were measured in an analysis of the end-to-end distance changes in the RTX domain. The method was complemented with circular dichroism spectroscopy, tryptophan fluorescence, and bis-ANS dye binding. High ionic strength was observed to decrease the calcium affinity of the RTX domain. A truncation and single amino acid mutations yielded insights into the structural determinants of beta roll formation. Mutating the conserved Asp residue in one of the nine repeats significantly reduced the affinity of the domains for calcium ions. Removal of the sequences flanking the repeat domain prevented folding, but replacing them with fluorescent proteins restored the conformational behavior, suggesting an entropic stabilization. The FRET-based method is a useful technique that complements other low-resolution techniques for investigating the dynamic conformational behavior of the RTX domain and other intrinsically disordered protein domains.
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Affiliation(s)
- Géza R Szilvay
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, USA
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62
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Thomas JM, Daugherty PS. Proligands with protease-regulated binding activity identified from cell-displayed prodomain libraries. Protein Sci 2009; 18:2053-9. [PMID: 19653300 DOI: 10.1002/pro.217] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A general method was developed for the discovery of protease-activated binding ligands, or proligands, from combinatorial prodomain libraries displayed on the surface of E. coli. Peptide libraries of candidate prodomains were fused with a matrix metalloprotease-2 substrate linker to a vascular endothelial growth factor-binding peptide and sorted using a two-stage flow cytometry screening procedure to isolate proligands that required protease treatment for binding activity. Prodomains that imparted protease-mediated switching activity were identified after three sorting cycles using two unique library design strategies. The best performing proligand exhibited a 100-fold improvement in apparent binding affinity after exposure to protease. This method may prove useful for developing therapeutic and diagnostic ligands with improved systemic targeting specificity.
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Affiliation(s)
- Jerry M Thomas
- Department of Chemical Engineering, University of California, Santa Barbara, 93106, USA
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63
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Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-Like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations. J Phys Chem B 2009; 113:15639-47. [DOI: 10.1021/jp9066718] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phanourios Tamamis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Emmanouil Kasotakis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Anna Mitraki
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
| | - Georgios Archontis
- Department of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus, and Department of Materials Science and Technology, University of Crete, and Institute for Electronic Structure and Laser, FORTH, Heraklion, Crete, Greece
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64
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Jones KS. Assays on the influence of biomaterials on allogeneic rejection in tissue engineering. TISSUE ENGINEERING PART B-REVIEWS 2009; 14:407-17. [PMID: 18826337 DOI: 10.1089/ten.teb.2008.0264] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In tissue engineering, innate responses to biomaterial scaffolds will affect rejection of allogeneic cells. Biomaterials directly influence innate and adaptive immune cell adhesion, reactive oxygen intermediate production, cytokine secretion, nuclear factor-kappa B nuclear translocation, gene expression, and cell surface markers, all of which are likely to affect allogeneic rejection responses. A major goal in tissue engineering is to induce transplant tolerance, potentially by manipulating the biomaterial component. This review describes methods of measuring responses of macrophages, dendritic cells, and T cells stimulated in vitro and in vivo and addresses key factors in assay development. Such tests include mixed leukocyte reactions, enzyme-linked immunosorbent spot assays, trans-vivo delayed-type hypersensitivity assays, and measurement of dendritic cell subsets and anti-donor antibodies; we propose extending these studies to tissue engineering.
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Affiliation(s)
- Kim S Jones
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada.
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65
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Gao S, Simon MJ, Morrison B, Banta S. Bifunctional chimeric fusion proteins engineered for DNA delivery: optimization of the protein to DNA ratio. Biochim Biophys Acta Gen Subj 2009; 1790:198-207. [PMID: 19402206 DOI: 10.1016/j.bbagen.2009.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Cell penetrating peptides (CPPs) have been used to deliver nucleotide-based therapeutics to cells, but this approach has produced mixed results. Ionic interactions and covalent bonds between the CPPs and the cargos may inhibit the effectiveness of the CPPs or interfere with the bioactivity of the cargos. METHODS We have created a bifunctional chimeric protein that binds DNA using the p50 domain of the NF-kappaB transcription factor and is functionalized for delivery with the TAT CPP. The green fluorescent protein (GFP) has been incorporated for tracking delivery. The new chimeric protein, p50-GFP-TAT, was compared to p50-GFP, GFP-TAT and GFP as controls for the ability to transduce PC12 cells with and without oligonucleotide cargos. RESULTS The p50-GFP-TAT construct can deliver 30 bp and 293 bp oligonucleotides to PC12 cells with an optimal ratio of 1.89 protein molecules per base pair of DNA length. This correlation was validated through the delivery of a fluorescent protein transgene encoded in a plasmid to PC12 cells. Thus, self-assembling CPP-based bifunctional fusion proteins can be engineered for the non-viral delivery of nucleotide-based cargos to mammalian cells. GENERAL SIGNIFICANCE This work represents an important step forward in the rational design of protein-based systems for the delivery of macromolecular cargos.
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Affiliation(s)
- Shan Gao
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
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66
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Development of a bacteriophage-based system for the selection of structured peptides. Anal Biochem 2009; 388:122-7. [DOI: 10.1016/j.ab.2009.01.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 01/28/2009] [Accepted: 01/29/2009] [Indexed: 02/05/2023]
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67
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Hansen M, Ruizendaal L, Löwik D, van Hest J. Switchable peptides. DRUG DISCOVERY TODAY. TECHNOLOGIES 2009; 6:e1-e40. [PMID: 24128990 DOI: 10.1016/j.ddtec.2009.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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68
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Bioelectrocatalytic hydrogels from electron-conducting metallopolypeptides coassembled with bifunctional enzymatic building blocks. Proc Natl Acad Sci U S A 2008; 105:15275-80. [PMID: 18824691 DOI: 10.1073/pnas.0805249105] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here, we present two bifunctional protein building blocks that coassemble to form a bioelectrocatalytic hydrogel that catalyzes the reduction of dioxygen to water. One building block, a metallopolypeptide based on a previously designed triblock polypeptide, is electron-conducting. A second building block is a chimera of artificial alpha-helical leucine zipper and random coil domains fused to a polyphenol oxidase, small laccase (SLAC). The metallopolypeptide has a helix-random-helix secondary structure and forms a hydrogel via tetrameric coiled coils. The helical and random domains are identical to those fused to the polyphenol oxidase. Electron-conducting functionality is derived from the divalent attachment of an osmium bis-bipyrdine complex to histidine residues within the peptide. Attachment of the osmium moiety is demonstrated by mass spectroscopy (MS-MALDI-TOF) and cyclic voltammetry. The structure and function of the alpha-helical domains are confirmed by circular dichroism spectroscopy and by rheological measurements. The metallopolypeptide shows the ability to make electrical contact to a solid-state electrode and to the redox centers of modified SLAC. Neat samples of the modified SLAC form hydrogels, indicating that the fused alpha-helical domain functions as a physical cross-linker. The fusion does not disrupt dimer formation, a necessity for catalytic activity. Mixtures of the two building blocks coassemble to form a continuous supramolecular hydrogel that, when polarized, generates a catalytic current in the presence of oxygen. The specific application of the system is a biofuel cell cathode, but this protein-engineering approach to advanced functional hydrogel design is general and broadly applicable to biocatalytic, biosensing, and tissue-engineering applications.
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69
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Luo Z, Zhao X, Zhang S. Structural dynamic of a self-assembling peptide d-EAK16 made of only D-amino acids. PLoS One 2008; 3:e2364. [PMID: 18509542 PMCID: PMC2387071 DOI: 10.1371/journal.pone.0002364] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 05/06/2008] [Indexed: 02/05/2023] Open
Abstract
We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25 degrees C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70 degrees C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80 degrees C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4 degrees C to 110 degrees C then cooling back from 110 degrees C to 4 degrees C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology.
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Affiliation(s)
- Zhongli Luo
- West China Hospital, Laboratory for Nanobiomedical Technology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaojun Zhao
- West China Hospital, Laboratory for Nanobiomedical Technology, Sichuan University, Chengdu, Sichuan, China
| | - Shuguang Zhang
- West China Hospital, Laboratory for Nanobiomedical Technology, Sichuan University, Chengdu, Sichuan, China
- * E-mail:
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70
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Blenner MA, Banta S. Characterization of the 4D5Flu single-chain antibody with a stimulus-responsive elastin-like peptide linker: a potential reporter of peptide linker conformation. Protein Sci 2008; 17:527-36. [PMID: 18218715 DOI: 10.1110/ps.073257308] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-chain antibodies (scFvs) are comprised of IgG variable light and variable heavy domains tethered together by a peptide linker whose length and sequence can affect antigen binding properties. The ability to modulate antigen binding affinity through the use of environmental triggers would be of great interest for many biotechnological applications. We have characterized the antigen binding properties of an anti-fluorescein scFv, 4D5Flu, containing stimulus-responsive short elastin-like peptide linkers and nonresponsive flexible linkers. Comparison of length-matched flexible and short elastin-like peptide linkers indicates that a stimulus-responsive linker can confer stimulus-responsive control of fluorescein binding. A linker length of either six or 10 amino acids proved to have the largest thermally induced response. Similar differences in binding free energy changes indicate a common underlying mechanism of thermal responsiveness. Contrary to the thermal behavior, the effect of salt, another elastin beta-turn-inducing stimulus, stabilized antigen binding in the six- and 10-amino-acid linkers such that elastin-like linkers became less stimulus-responsive as compared with flexible linkers. Again, the thermodynamic analysis indicates a common mechanism of salt responsiveness. Characterization of the room-temperature binding affinities and evidence indicating a dimeric state of the scFvs concomitantly suggest the major contribution to the stimulus-responsive behavior derives from the perturbation of interdomain associations, rather than the linker-constrained disruption of the intramolecular association. The ability to use stimulus-responsive peptide modules to exert a novel control over protein function will likely find application in the creation of allosteric antibodies and scFv-based biosensors, and as a platform to enable the evolution of new stimulus-responsive peptides.
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71
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Shah NH, Kirshenbaum K. Photoresponsive peptoid oligomers bearing azobenzene side chains. Org Biomol Chem 2008; 6:2516-21. [DOI: 10.1039/b804802a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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72
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Wheeldon IR, Barton SC, Banta S. Bioactive proteinaceous hydrogels from designed bifunctional building blocks. Biomacromolecules 2007; 8:2990-4. [PMID: 17887795 DOI: 10.1021/bm700858p] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Stimulus-responsive, or "smart" protein-based hydrogels are of interest for many bioengineering applications, but have yet to include biological activity independent of structural functionality. We have genetically engineered bifunctional building blocks incorporating fluorescent proteins that self-assemble into robust and active hydrogels. Gelation occurs when protein building blocks are cross-linked through native protein-protein interactions and the aggregation of alpha-helical hydrogel-forming appendages. Building blocks constructed from different fluorescent proteins can be mixed to enable tuning of fluorescence loading and hydrogel strength with a high degree of independence. FRET experiments suggest a macro-homogeneous structure and that intragel and interprotein reactions can be engineered. This design approach will enable the facile construction of complex hydrogels with broad applicability.
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Affiliation(s)
- Ian R Wheeldon
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY 10027, USA
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