51
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Maynard SJ, Almeida AM, Yoshimi Y, Gellman SH. New charge-bearing amino acid residues that promote β-sheet secondary structure. J Am Chem Soc 2014; 136:16683-8. [PMID: 25393077 PMCID: PMC4277779 DOI: 10.1021/ja510265e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Proteinogenic
amino acid residues that promote β-sheet secondary
structure are hydrophobic (e.g., Ile or Val) or only moderately polar
(e.g., Thr). The design of peptides intended to display β-sheet
secondary structure in water typically requires one set of residues
to ensure conformational stability and an orthogonal set, with charged
side chains, to ensure aqueous solubility and discourage self-association.
Here we describe new amino acids that manifest substantial β-sheet
propensity, by virtue of β-branching, and also bear an ionizable
group in the side chain.
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Affiliation(s)
- Stacy J Maynard
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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52
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Ginovska-Pangovska B, Dutta A, Reback ML, Linehan JC, Shaw WJ. Beyond the active site: the impact of the outer coordination sphere on electrocatalysts for hydrogen production and oxidation. Acc Chem Res 2014; 47:2621-30. [PMID: 24945095 DOI: 10.1021/ar5001742] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Redox active metalloenzymes play a major role in energy transformation reactions in biological systems. Examples include formate dehydrogenases, nitrogenases, CO dehydrogenase, and hydrogenases. Many of these reactions are also of interest to humans as potential energy storage or utilization reactions for photoelectrochemical, electrolytic, and fuel cell applications. These metalloenzymes consist of redox active metal centers where substrates are activated and undergo transformation to products accompanied by electron and proton transfer to or from the substrate. These active sites are typically buried deep within a protein matrix of the enzyme with channels for proton transport, electron transport, and substrate/product transport between the active site and the surface of the protein. In addition, there are amino acid residues that lie in close proximity to the active site that are thought to play important roles in regulating and enhancing enzyme activity. Directly studying the outer coordination sphere of enzymes can be challenging due to their complexity, and the use of modified molecular catalysts may allow us to provide some insight. There are two fundamentally different approaches to understand these important interactions. The "bottom-up" approach involves building an amino acid or peptide containing outer coordination sphere around a functional molecular catalyst, and the "top-down" approach involves attaching molecular catalyst to a structured protein. Both of these approaches have been undertaken for hydrogenase mimics and are the emphasis of this Account. Our focus has been to utilize amino acid or peptide based scaffolds on an active functional enzyme mimic for H2 oxidation and production, [Ni(P(R)2N(R('))2)2](2+). This "bottom-up" approach has allowed us to evaluate individual functional group and structural contributions to electrocatalysts for H2 oxidation and production. For instance, using amine, ether, and carboxylic acid functionalities in the outer coordination sphere enhances proton movement and results in lower catalytic overpotentials for H2 oxidation, while achieving water solubility in some cases. Amino acids with acidic and basic side chains concentrate substrate around catalysts for H2 production, resulting in up to 5-fold enhancements in rate. The addition of a structured peptide in an H2 production catalyst limited the structural freedom of the amino acids nearest the active site, while enhancing the overall rate. Enhanced stability to oxygen or extreme conditions such as strongly acidic or basic conditions has also resulted from an amino acid based outer coordination sphere. From the "top-down" approach, others have achieved water solubility and photocatalytic activity by associating this core complex with photosystem-I. Collectively, by use of this well understood core, the role of individual and combined features of the outer coordination sphere are starting to be understood at a mechanistic level. Common mechanisms have yet to be defined to predictably control these processes, but our growing knowledge in this area is essential for the eventual mimicry of enzymes by efficient molecular catalysts for practical use.
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Affiliation(s)
| | - Arnab Dutta
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Matthew L. Reback
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - John C. Linehan
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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53
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Kier BL, Andersen NH. Captides: rigid junctions between beta sheets and small molecules. J Pept Sci 2014; 20:704-15. [PMID: 24909552 DOI: 10.1002/psc.2657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 12/15/2022]
Abstract
An extensive series of covalently linked small molecule-peptide adducts based on a terminally capped-beta hairpin motif is reported. The constructs can be prepared by standard solid-phase Fmoc chemistry with one to four peptide chains linked to small molecule hubs bearing carboxylic acid moieties. The key feature of interest is the precise, buried environment of the small molecule, and its rigid orientation relative to one or more short but fully structured peptide chain(s). Most of this study employs a minimalist nine residue 'captide', a capped β-turn, but we illustrate general applicability to peptides which can terminate in a beta strand. The non-peptide portion of these adducts can include nearly any molecule bearing one or more carboxylic acid groups. Fold-dependent rigidity sets this strategy apart from the currently available bioconjugation methods, which typically engender significant flexibility between peptide and tag. Applications to catalyst enhancement, drug design, higher-order assembly, and FRET calibration rulers are discussed.
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Affiliation(s)
- Brandon L Kier
- University of Washington - Chemistry, Bagley Hall Room 205 Box 351700, Seattle, WA, 98195-1700, USA
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54
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Reback ML, Buchko GW, Kier BL, Ginovska-Pangovska B, Xiong Y, Lense S, Hou J, Roberts JAS, Sorensen CM, Raugei S, Squier TC, Shaw WJ. Enzyme design from the bottom up: an active nickel electrocatalyst with a structured peptide outer coordination sphere. Chemistry 2014; 20:1510-4. [PMID: 24443316 DOI: 10.1002/chem.201303976] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Indexed: 11/07/2022]
Abstract
Catalytic, peptide-containing metal complexes with a well-defined peptide structure have the potential to enhance molecular catalysts through an enzyme-like outer coordination sphere. Here, we report the synthesis and characterization of an active, peptide-based metal complex built upon the well-characterized hydrogen production catalyst [Ni(P(Ph)2N(Ph))2](2+) (P(Ph)2N(Ph)=1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane). The incorporated peptide maintains its β-hairpin structure when appended to the metal core, and the electrocatalytic activity of the peptide-based metal complex (≈100,000 s(-1)) is enhanced compared to the parent complex ([Ni(P(Ph)2N(APPA))2](2+); ≈50,500 s(-1)). The combination of an active molecular catalyst with a structured peptide provides a scaffold that permits the incorporation of features of an enzyme-like outer-coordination sphere necessary to create molecular electrocatalysts with enhanced functionality.
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55
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Kier BL, Anderson JM, Andersen NH. Circular permutation of a WW domain: folding still occurs after excising the turn of the folding-nucleating hairpin. J Am Chem Soc 2014; 136:741-9. [PMID: 24350581 PMCID: PMC4051316 DOI: 10.1021/ja410824x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A hyperstable Pin1 WW domain has been circularly permuted via excision of the fold-nucleating turn; it still folds to form the native three-strand sheet and hydrophobic core features. Multiprobe folding dynamics studies of the normal and circularly permuted sequences, as well as their constituent hairpin fragments and comparable-length β-strand-loop-β-strand models, indicate 2-state folding for all topologies. N-terminal hairpin formation is the fold nucleating event for the wild-type sequence; the slower folding circular permutant has a more distributed folding transition state.
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Affiliation(s)
- Brandon L. Kier
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | | | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, WA 98195
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56
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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57
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Jimenez-Cruz CA, Garcia AE. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin. Phys Chem Chem Phys 2014; 16:6422-9. [DOI: 10.1039/c3cp54336f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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58
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β-Hairpin protein epitope mimetic technology in drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 9:e1-e70. [PMID: 24064246 DOI: 10.1016/j.ddtec.2011.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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59
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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60
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Bhat HB, Kishimoto T, Abe M, Makino A, Inaba T, Murate M, Dohmae N, Kurahashi A, Nishibori K, Fujimori F, Greimel P, Ishitsuka R, Kobayashi T. Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains. J Lipid Res 2013; 54:2933-43. [PMID: 23918047 DOI: 10.1194/jlr.d041731] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A mixture of sphingomyelin (SM) and cholesterol (Chol) exhibits a characteristic lipid raft domain of the cell membranes that provides a platform to which various signal molecules as well as virus and bacterial proteins are recruited. Several proteins capable of specifically binding either SM or Chol have been reported. However, proteins that selectively bind to SM/Chol mixtures are less well characterized. In our screening for proteins specifically binding to SM/Chol liposomes, we identified a novel ortholog of Pleurotus ostreatus, pleurotolysin (Ply)A, from the extract of edible mushroom Pleurotus eryngii, named PlyA2. Enhanced green fluorescent protein (EGFP)-conjugated PlyA2 bound to SM/Chol but not to phosphatidylcholine/Chol liposomes. Cell surface labeling of PlyA2-EGFP was abolished after sphingomyelinase as well as methyl-β-cyclodextrin treatment, removing SM and Chol, respectively, indicating that PlyA2-EGFP specifically binds cell surface SM/Chol rafts. Tryptophan to alanine point mutation of PlyA2 revealed the importance of C-terminal tryptophan residues for SM/Chol binding. Our results indicate that PlyA2-EGFP is a novel protein probe to label SM/Chol lipid domains both in cell and model membranes.
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Affiliation(s)
- Hema Balakrishna Bhat
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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61
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Shu I, Scian M, Stewart JM, Kier BL, Andersen NH. 13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues. JOURNAL OF BIOMOLECULAR NMR 2013; 56:313-329. [PMID: 23851979 DOI: 10.1007/s10858-013-9749-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
The present studies have shown that (13)C=O, (13)C(α) and (13)C(β) of H-bonded strand residues in β-hairpins provide additional probes for quantitating the extent of folding in β-hairpins and other β-sheet models. Large differences in the structuring shifts (CSDs) of these (13)C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three (13)C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from (13)C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the (13)C' and (13)C(β) CSDs will provide the best differentiation with 100%-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein β-sheets. Our survey of reported (13)C shifts in β-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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62
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Jimenez-Cruz CA, Garcia AE. Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations. J Chem Theory Comput 2013; 9:3750-5. [DOI: 10.1021/ct400170x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Camilo Andres Jimenez-Cruz
- Department of Physics,
Applied Physics and Astronomy,
and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180,
United States
| | - Angel E. Garcia
- Department of Physics,
Applied Physics and Astronomy,
and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180,
United States
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63
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Mahajan M, Bhattacharjya S. β-Hairpin peptides: heme binding, catalysis, and structure in detergent micelles. Angew Chem Int Ed Engl 2013; 52:6430-4. [PMID: 23640811 DOI: 10.1002/anie.201300241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/25/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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64
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Mahajan M, Bhattacharjya S. β-Hairpin Peptides: Heme Binding, Catalysis, and Structure in Detergent Micelles. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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65
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Kar K, Hoop CL, Drombosky KW, Baker MA, Kodali R, Arduini I, van der Wel PCA, Horne WS, Wetzel R. β-hairpin-mediated nucleation of polyglutamine amyloid formation. J Mol Biol 2013; 425:1183-97. [PMID: 23353826 PMCID: PMC3602386 DOI: 10.1016/j.jmb.2013.01.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 12/01/2022]
Abstract
The conformational preferences of polyglutamine (polyQ) sequences are of major interest because of their central importance in the expanded CAG repeat diseases that include Huntington's disease. Here, we explore the response of various biophysical parameters to the introduction of β-hairpin motifs within polyQ sequences. These motifs (tryptophan zipper, disulfide, d-Pro-Gly, Coulombic attraction, l-Pro-Gly) enhance formation rates and stabilities of amyloid fibrils with degrees of effectiveness well correlated with their known abilities to enhance β-hairpin formation in other peptides. These changes led to decreases in the critical nucleus for amyloid formation from a value of n=4 for a simple, unbroken Q23 sequence to approximate unitary n values for similar length polyQs containing β-hairpin motifs. At the same time, the morphologies, secondary structures, and bioactivities of the resulting fibrils were essentially unchanged from simple polyQ aggregates. In particular, the signature pattern of solid-state NMR (13)C Gln resonances that appears to be unique to polyQ amyloid is replicated exactly in fibrils from a β-hairpin polyQ. Importantly, while β-hairpin motifs do produce enhancements in the equilibrium constant for nucleation in aggregation reactions, these Kn values remain quite low (~10(-)(10)) and there is no evidence for significant enhancement of β-structure within the monomer ensemble. The results indicate an important role for β-turns in the nucleation mechanism and structure of polyQ amyloid and have implications for the nature of the toxic species in expanded CAG repeat diseases.
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Affiliation(s)
- Karunakar Kar
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
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66
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Scian M, Shu I, Olsen KA, Hassam K, Andersen NH. Mutational effects on the folding dynamics of a minimized hairpin. Biochemistry 2013; 52:2556-64. [PMID: 23521619 DOI: 10.1021/bi400146c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The fold stabilities and folding dynamics of a series of mutants of a model hairpin, KTW-NPATGK-WTE (HP7), are reported. The parent system and the corresponding DPATGK loop species display submicrosecond folding time constants. The mutational studies revealed that ultrafast folding requires both some prestructuring of the loop and a favorable interaction between the chain termini in the transition state. In the case of YY-DPETGT-WY, another submicrosecond folding species [Davis, C. M., Xiao, S., Raleigh, D. P., and Dyer, R. B. (2012) J. Am. Chem. Soc. 134, 14476-14482], a hydrophobic cluster provides the latter. In the case of HP7, the Coulombic interaction between the terminal NH3(+) and CO2(-) units provides this; a C-terminal Glu to amidated Ala mutation results in a 5-fold retardation of the folding rate. The effects of mutations within the reversing loop indicate the balance between loop flexibility (favoring fast conformational searching) and turn formation in the unfolded state is a major factor in determining the folding dynamics. The -NAAAKX- loops examined display no detectable turn formation propensity in other hairpin constructs but do result in stable analogues of HP7. Peptide KTW-NAAAKK-WTE displays the same fold stability as HP7, but both the folding and unfolding time constants are greater by a factor of 20.
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Affiliation(s)
- Michele Scian
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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67
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McMillan AW, Kier BL, Shu I, Byrne A, Andersen NH, Parson WW. Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations. J Phys Chem B 2013; 117:1790-809. [PMID: 23330783 PMCID: PMC3581364 DOI: 10.1021/jp3097378] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The quantum yield of tryptophan (Trp) fluorescence was measured in 30 designed miniproteins (17 β-hairpins and 13 Trp-cage peptides), each containing a single Trp residue. Measurements were made in D(2)O and H(2)O to distinguish between fluorescence quenching mechanisms involving electron and proton transfer in the hairpin peptides, and at two temperatures to check for effects of partial unfolding of the Trp-cage peptides. The extent of folding of all the peptides also was measured by NMR. The fluorescence yields ranged from 0.01 in some of the Trp-cage peptides to 0.27 in some hairpins. Fluorescence quenching was found to occur by electron transfer from the excited indole ring of the Trp to a backbone amide group or the protonated side chain of a nearby histidine, glutamate, aspartate, tyrosine, or cysteine residue. Ionized tyrosine side chains quenched strongly by resonance energy transfer or electron transfer to the excited indole ring. Hybrid classical/quantum mechanical molecular dynamics simulations were performed by a method that optimized induced electric dipoles separately for the ground and excited states in multiple π-π* and charge-transfer (CT) excitations. Twenty 0.5 ns trajectories in the tryptophan's lowest excited singlet π-π* state were run for each peptide, beginning by projections from trajectories in the ground state. Fluorescence quenching was correlated with the availability of a CT or exciton state that was strongly coupled to the π-π* state and that matched or fell below the π-π* state in energy. The fluorescence yields predicted by summing the calculated rates of charge and energy transfer are in good accord with the measured yields.
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Affiliation(s)
- Andrew W. McMillan
- Department of Biochemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - Brandon L. Kier
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - Irene Shu
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
| | - Aimee Byrne
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
| | - Niels H. Andersen
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - William W. Parson
- Department of Biochemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
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68
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Pehere AD, Sumby CJ, Abell AD. New cylindrical peptide assemblies defined by extended parallel β-sheets. Org Biomol Chem 2013; 11:425-9. [DOI: 10.1039/c2ob26637g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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69
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Han S, Kim D, Han SH, Kim NH, Kim SH, Lim YB. Structural and Conformational Dynamics of Self-Assembling Bioactive β-Sheet Peptide Nanostructures Decorated with Multivalent RNA-Binding Peptides. J Am Chem Soc 2012; 134:16047-53. [DOI: 10.1021/ja307493t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sanghun Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Donghun Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Nam Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Sun Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
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70
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Almeida AM, Li R, Gellman SH. Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking. J Am Chem Soc 2012; 134:75-8. [PMID: 22148521 PMCID: PMC3266109 DOI: 10.1021/ja208856c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Disulfide bonds between Cys residues in adjacent strands of parallel β-sheets are rare among proteins, which suggests that parallel β-sheet structure is not stabilized by such disulfide cross-links. We report experimental results that show, surprisingly, that an interstrand disulfide bond can stabilize parallel β-sheets formed by an autonomously folding peptide in aqueous solution. NMR analysis reveals that parallel β-sheet structure is terminated beyond the disulfide bond, which causes deviation from the extended backbone conformation at one of the Cys residues.
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Affiliation(s)
- Aaron M. Almeida
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
| | - Rebecca Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
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71
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Huggins KNL, Bisaglia M, Bubacco L, Tatarek-Nossol M, Kapurniotu A, Andersen NH. Designed hairpin peptides interfere with amyloidogenesis pathways: fibril formation and cytotoxicity inhibition, interception of the preamyloid state. Biochemistry 2011; 50:8202-12. [PMID: 21848289 DOI: 10.1021/bi200760h] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hairpin peptides bearing cross-strand Trp-Trp and Tyr-Tyr pairs at non-H-bonded strand sites modulate the aggregation of two unrelated amyloidogenic systems, human pancreatic amylin (hAM) and α-synuclein (α-syn), associated with type II diabetes and Parkinson's disease, respectively. In the case of hAM, we have previously reported that inhibition of amyloidogenesis is observed as an increase in the lag time to amyloid formation and a diminished thioflavin (ThT) fluorescence response. In this study, a reduced level of hAM fibril formation is confirmed by transmission electron microscopy imaging. Several of the hairpins tested were significantly more effective inhibitors than rat amylin. Moreover, a marked inhibitory effect on hAM-associated cytotoxicity by the more potent hairpin peptide is demonstrated. In the case of α-syn, the dominant effect of active hairpins was, besides a weakened ThT fluorescence response, the earlier appearance of insoluble aggregates that do not display amyloid characteristics with the few fibrils observed having abnormal morphology. We attribute the alteration of the α-synuclein aggregation pathway observed to the capture of a preamyloid state and diversion to nonamyloidogenic aggregates. These β-hairpins represent a new class of amyloid inhibitors that bear no sequence similarity to the amyloid-producing polypeptides that are inhibited. A mechanistic rationale for these effects is proposed.
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Affiliation(s)
- Kelly N L Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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72
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Freire F, Almeida AM, Fisk JD, Steinkruger JD, Gellman SH. Impact of strand length on the stability of parallel-β-sheet secondary structure. Angew Chem Int Ed Engl 2011; 50:8735-8. [PMID: 21812082 DOI: 10.1002/anie.201102986] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Felix Freire
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Av., Madison, WI 53726, USA
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73
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Freire F, Almeida AM, Fisk JD, Steinkruger JD, Gellman SH. Impact of Strand Length on the Stability of Parallel-β-Sheet Secondary Structure. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102986] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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74
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Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Proteins 2011; 79:244-60. [PMID: 21058397 DOI: 10.1002/prot.22878] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity.
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Affiliation(s)
- S Indu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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75
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Shu I, Stewart JM, Scian M, Kier BL, Andersen NH. β-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins. J Am Chem Soc 2011; 133:1196-9. [PMID: 21214243 DOI: 10.1021/ja1088953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (13)C chemical shifts measured for designed β-hairpins indicate that the structuring shifts (upfield for Cα and C', downfield for Cβ) previously reported as diagnostic for β-structuring in proteins appear only at the H-bonded strand residues. The resulting periodicity of structuring shift magnitudes is not, however, a consequence of H-bonding status; rather, it reflects a previously unrecognized alternation in the backbone torsion angles of β-strands. This feature of hairpins is also likely to be present in proteins. The study provides reference values for the expectation shifts for (13)C sites in β-structures that should prove useful in the characterization of the folding equilibria of β-sheet models.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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76
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Santiveri CM, Pérez de Vega MJ, González-Muñiz R, Jiménez MA. Trp-Trp pairs as β-hairpin stabilisers: Hydrogen-bonded versus non-hydrogen-bonded sites. Org Biomol Chem 2011; 9:5487-92. [DOI: 10.1039/c1ob05353a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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