1
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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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2
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Kundert K, Kortemme T. Computational design of structured loops for new protein functions. Biol Chem 2019; 400:275-288. [PMID: 30676995 PMCID: PMC6530579 DOI: 10.1515/hsz-2018-0348] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022]
Abstract
The ability to engineer the precise geometries, fine-tuned energetics and subtle dynamics that are characteristic of functional proteins is a major unsolved challenge in the field of computational protein design. In natural proteins, functional sites exhibiting these properties often feature structured loops. However, unlike the elements of secondary structures that comprise idealized protein folds, structured loops have been difficult to design computationally. Addressing this shortcoming in a general way is a necessary first step towards the routine design of protein function. In this perspective, we will describe the progress that has been made on this problem and discuss how recent advances in the field of loop structure prediction can be harnessed and applied to the inverse problem of computational loop design.
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Affiliation(s)
- Kale Kundert
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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3
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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4
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Soranno A, Cabassi F, Orselli ME, Cellmer T, Gori A, Longhi R, Buscaglia M. Dynamics of Structural Elements of GB1 β-Hairpin Revealed by Tryptophan-Cysteine Contact Formation Experiments. J Phys Chem B 2018; 122:11468-11477. [PMID: 30215522 DOI: 10.1021/acs.jpcb.8b07399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quenching of the triplet state of tryptophan by close contact with cysteine provides a tool for measuring the rate of intramolecular contact formation, one of the most elementary events in the folding process, in peptides and proteins using only natural probes. Here we present a study performed on a stabilized mutant of the second β-hairpin of the GB1 domain, where we combine steady-state fluorescence, laser-induced temperature-jump, and contact formation measurements to unveil the role of elementary structural components on hairpin dynamics and overall stability. In particular, our methodology provides access to the conformational dynamics of both the folded and unfolded state of the hairpin under native conditions, revealing the presence of extremely slow dynamics on the microsecond time scale in the unfolded state and coexistence of structures with partial pairing of the tails in the folded state. Comparing model peptides that mimic the turn sequence, we found that both ion pairing and hydrogen bonding due to the threonine side chain contribute to the propensity of turn formation but not to the much slower dynamics of the hydrophobic core formation. Interestingly, the dynamics of the turn region in isolation are significantly faster than the dynamics measured for the unfolded state of the complete hairpin, suggesting that non-native hydrophobic contacts slow down the reconfiguration dynamics of the unfolded state. Overall, the information extracted from these experiments provides kinetic limits on interconversions among conformational populations, hence enabling a simplified multistate free-energy landscape for the GB1 hairpin to be drawn.
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Affiliation(s)
- Andrea Soranno
- Department of Biochemistry and Molecular Biophysics , Washington University in St. Louis , St. Louis , Missouri 63130 , United States
| | - Francesca Cabassi
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
| | - Maria Elena Orselli
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
| | - Troy Cellmer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare , Consiglio Nazionale delle Ricerche , 20131 Milano , Italy
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare , Consiglio Nazionale delle Ricerche , 20131 Milano , Italy
| | - Marco Buscaglia
- Department of Medical Biotechnology and Translational Medicine , Università degli Studi di Milano , 20122 Milano , Italy
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5
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Maximova K, Venken T, Reuter N, Trylska J. d-Peptides as inhibitors of PR3-membrane interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:458-466. [PMID: 29132840 DOI: 10.1016/j.bbamem.2017.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/02/2017] [Accepted: 11/07/2017] [Indexed: 01/08/2023]
Abstract
Proteinase 3 (PR3) is a neutrophil serine protease present in cytoplasmic granules but also expressed at the neutrophil surface where it mediates proinflammatory effects. Studies of the underlying molecular mechanisms have been hampered by the lack of inhibitors of the PR3 membrane anchorage. Indeed while there exist inhibitors of the catalytic activity of PR3, its membrane interfacial binding site (IBS) is distinct from its catalytic site. The IBS has been characterized both by mutagenesis experiments and molecular modeling. Through docking and molecular dynamics simulations we have designed d-peptides targeting the PR3 IBS. We used surface plasmon resonance to evaluate their effect on the binding of PR3 to phospholipid bilayers. Next, we verified their ability of binding to PR3 via fluorescence spectroscopy and isothermal titration calorimetry. The designed peptides did not affect the catalytic activity of PR3. A few peptides bound to PR3 hydrophobic pockets and inhibited PR3 binding to lipids. While the (KFF)3K d-peptide inconveniently showed a significant affinity for the lipids, another d-peptide (SAKEAFFKLLAS) did not and it inhibited the PR3-membrane binding site with IC50 of about 40μM. Our work puts forward d-peptides as promising inhibitors of peripheral protein-membrane interactions, which remain high-hanging fruits in drug design.
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Affiliation(s)
- Ksenia Maximova
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Tom Venken
- Department of Molecular Biology, University of Bergen, 5008 Bergen, Norway; Flemish Institute for Technological Research, VITO, B-2400 Mol, Belgium
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, 5008 Bergen, Norway.
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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6
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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7
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Kar K, Baker MA, Lengyel GA, Hoop CL, Kodali R, Byeon IJ, Horne WS, van der Wel PCA, Wetzel R. Backbone Engineering within a Latent β-Hairpin Structure to Design Inhibitors of Polyglutamine Amyloid Formation. J Mol Biol 2016; 429:308-323. [PMID: 27986569 DOI: 10.1016/j.jmb.2016.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/03/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
Candidates for the toxic molecular species in the expanded polyglutamine (polyQ) repeat diseases range from various types of aggregates to "misfolded" monomers. One way to vet these candidates is to develop mutants that restrict conformational landscapes. Previously, we inserted two self-complementary β-hairpin enhancing motifs into a short polyQ sequence to generate a mutant, here called "βHP," that exhibits greatly improved amyloid nucleation without measurably enhancing β-structure in the monomer ensemble. We extend these studies here by introducing single-backbone H-bond impairing modifications αN-methyl Gln or l-Pro at key positions within βHP. Modifications predicted to allow formation of a fully H-bonded β-hairpin at the fibril edge while interfering with H-bonding to the next incoming monomer exhibit poor amyloid formation and act as potent inhibitors in trans of simple polyQ peptide aggregation. In contrast, a modification that disrupts intra-β-hairpin H-bonding within βHP, while also aggregating poorly, is ineffective at inhibiting amyloid formation in trans. The inhibitors constitute a dynamic version of the edge-protection negative design strategy used in protein evolution to limit unwanted protein aggregation. Our data support a model in which polyQ peptides containing strong β-hairpin encouraging motifs only rarely form β-hairpin conformations in the monomer ensemble, but nonetheless take on such conformations at key steps during amyloid formation. The results provide insights into polyQ solution structure and fibril formation while also suggesting an approach to the design of inhibitors of polyQ amyloid growth that focuses on conformational requirements for fibril and nucleus elongation.
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Affiliation(s)
- Karunakar Kar
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Matthew A Baker
- Department of Chemistry, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - George A Lengyel
- Department of Chemistry, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Ravindra Kodali
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - In-Ja Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Ronald Wetzel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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8
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Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
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Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
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9
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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10
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Raghavender US. Ultrafast folding and molecular dynamics of a linear hydrophobic β-hairpin. J Biomol Struct Dyn 2013; 31:1404-10. [DOI: 10.1080/07391102.2012.738612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Liu HL, Lin YM. Stability and Unfolding Mechanism of the N-terminal β-Hairpin from [2Fe-2S] Ferredoxin I by Molecular Dynamics Simulations. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200300112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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13
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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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14
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Engin O, Sayar M. Adsorption, Folding, and Packing of an Amphiphilic Peptide at the Air/Water Interface. J Phys Chem B 2012; 116:2198-207. [DOI: 10.1021/jp206327y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ozge Engin
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
| | - Mehmet Sayar
- College of Engineering, Koç University, 34450, Istanbul,
Turkey
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15
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Galeazzi R, Martelli G, Mazzanti A, Orena M, Rinaldi S. Quaternary Centres as a Tool for Modulating Foldamer Conformation. Chemistry 2011; 17:12564-8. [DOI: 10.1002/chem.201102103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Indexed: 11/11/2022]
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16
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Topilina NI, Ermolenkov VV, Sikirzhytski V, Higashiya S, Lednev IK, Welch JT. A de novo designed 11 kDa polypeptide: model for amyloidogenic intrinsically disordered proteins. Biopolymers 2010; 93:607-18. [PMID: 20162724 DOI: 10.1002/bip.21412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A de novo polypeptide GH(6)[(GA)(3)GY(GA)(3)GE](8)GAH(6) (YE8) has a significant number of identical weakly interacting beta-strands with the turns and termini functionalized by charged amino acids to control polypeptide folding and aggregation. YE8 exists in a soluble, disordered form at neutral pH but is responsive to changes in pH and ionic strength. The evolution of YE8 secondary structure has been successfully quantified during all stages of polypeptide fibrillation by deep UV resonance Raman (DUVRR) spectroscopy combined with other morphological, structural, spectral, and tinctorial characterization. The YE8 folding kinetics at pH 3.5 are strongly dependent on polypeptide concentration with a lag phase that can be eliminated by seeding with a solution of folded fibrillar YE8. The lag phase of polypeptide folding is concentration dependent leading to the conclusion that beta-sheet folding of the 11-kDa amyloidogenic polypeptide is completely aggregation driven.
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Affiliation(s)
- Natalya I Topilina
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
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17
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Wathen B, Jia Z. Protein beta-sheet nucleation is driven by local modular formation. J Biol Chem 2010; 285:18376-84. [PMID: 20382979 DOI: 10.1074/jbc.m110.120824] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite its central role in the protein folding process, the specific mechanism(s) behind beta-sheet formation has yet to be determined. For example, whether the nucleation of beta-sheets, often containing strands separated in sequence by many residues, is local or not remains hotly debated. Here, we investigate the initial nucleation step of beta-sheet formation by performing an analysis of the smallest beta-sheets in a non-redundant dataset on the grounds that the smallest sheets, having undergone little growth after nucleation, will be enriched for nucleating characteristics. We find that the residue propensities are similar for small and large beta-sheets as are their interstrand pairing preferences, suggesting that nucleation is not primarily driven by specific residues or interacting pairs. Instead, an examination of the structural environments of the two-stranded sheets shows that virtually all of them are contained in single, compact structural modules, or when multiple modules are present, one or both of the chain termini are involved. We, therefore, find that beta-nucleation is a local phenomenon resulting either from sequential or topological proximity. We propose that beta-nucleation is a result of two opposite factors; that is, the relative rigidity of an associated folding module that holds two stretches of coil close together in topology coupled with sufficient chain flexibility that enables the stretches of coil to bring their backbones in close proximity. Our findings lend support to the hydrophobic zipper model of protein folding (Dill, K. A., Fiebig, K. M., and Chan, H. S. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 1942-1946). Implications for protein folding are discussed.
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Affiliation(s)
- Brent Wathen
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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18
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Rabong C, Jordis U, Phopase JB. NXO Building Blocks for Backbone Modification of Peptides and Preparation of Pseudopeptides. J Org Chem 2010; 75:2492-500. [DOI: 10.1021/jo902518r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Jaywant B. Phopase
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
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19
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Isozaki K, Miki K. Design, synthesis, and complementary recognition of beta-hairpin peptides stabilized by artificial DNA base-pairing amino acids. Chem Commun (Camb) 2010; 46:2947-9. [PMID: 20386832 DOI: 10.1039/b924239b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel DNA base-pairing beta-hairpin peptide involving intramolecular hydrogen bonds for induction of beta-hairpin secondary structure and intermolecular complementary hydrogen bonds between thymine and diaminopyridine for molecular recognition has been synthesized.
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Affiliation(s)
- Katsuhiro Isozaki
- Organic Nanomaterials Center, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
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20
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Freire F, Gellman SH. Macrocyclic design strategies for small, stable parallel beta-sheet scaffolds. J Am Chem Soc 2009; 131:7970-2. [PMID: 19456161 DOI: 10.1021/ja902210f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pairs of short peptide strands can be induced to adopt an antiparallel beta-sheet secondary structure in aqueous solution via a macrocyclic constraint, as illustrated by many natural and designed peptides. We show that an analogous strategy is successful for creation of small units of parallel beta-sheet secondary structure in aqueous solution. Cyclization in this case requires nonpeptide segments for N-to-N and C-to-C interstrand linkage. Surprisingly, we find that only one of these segments needs to be preorganized.
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Affiliation(s)
- Felix Freire
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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21
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Monti D, Riva S. Natural and Artificial Microenzymes: Is It Possible to have Small and Efficient Biocatalysts? BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420109003643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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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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23
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Mirassou Y, Santiveri CM, Pérez de Vega MJ, González-Muñiz R, Jiménez MA. Disulfide Bonds versus Trp⋅⋅⋅Trp Pairs in Irregular β-Hairpins: NMR Structure of Vammin Loop 3-Derived Peptides as a Case Study. Chembiochem 2009; 10:902-10. [DOI: 10.1002/cbic.200800834] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Sharma GV, Rao KS, Ravi R, Narsimulu K, Nagendar P, Chandramouli C, Kumar SK, Kunwar A. Synthesis ofβ-Peptides withβ-Helices from New C-Linked Carbo-β-Amino Acids: Study on the Impact of Carbohydrate Side Chains. Chem Asian J 2009; 4:181-93. [DOI: 10.1002/asia.200800249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Wang J, McElheny D, Fu Y, Li G, Kim J, Zhou Z, Wu L, Keiderling TA, Hammer RP. A 310-helical pentapeptide in water: Interplay of α,α-disubstituted amino acids and the central residue on structure formation. Biopolymers 2009; 92:452-64. [DOI: 10.1002/bip.21258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Razkin J, Lindgren J, Nilsson H, Baltzer L. Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs. Chembiochem 2008; 9:1975-84. [PMID: 18600814 DOI: 10.1002/cbic.200800057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.
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Affiliation(s)
- Jesus Razkin
- Department of Applied Chemistry, Public University of Navarra, 31006 Pamplona, Navarra, Spain.
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27
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Bour P, Kim J, Kapitan J, Hammer RP, Huang R, Wu L, Keiderling TA. Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide. Chirality 2008; 20:1104-19. [DOI: 10.1002/chir.20560] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Abstract
Beta-sheets consist of extended polypeptide strands (beta-strands) connected by a network of hydrogen bonds and occur widely in proteins. Although the importance of beta-sheets in the folded structures of proteins has long been recognized, there is a growing recognition of the importance of intermolecular interactions among beta-sheets. Intermolecular interactions between the hydrogen-bonding edges of beta-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation. The importance of beta-sheet interactions in biological processes makes them potential targets for intervention in diseases such as AIDS, cancer, and Alzheimer's disease. This Account describes my research group's use of chemical model systems to study the structure and interactions of beta-sheets. Chemical model systems provide an excellent vehicle with which to explore beta-sheets, because they are smaller, simpler, and easier to manipulate than proteins. Synthetic chemical models also provide the opportunity to control or modulate natural systems or to develop other useful applications and may eventually lead to new drugs with which to treat diseases. In our "artificial beta-sheets", molecular template and turn units are combined with peptides to mimic the structures of parallel and antiparallel beta-sheets. The templates and turn units form folded, hydrogen-bonded structures with the peptide groups and help prevent the formation of complex, ill-defined aggregates. Templates that duplicate the hydrogen-bonding pattern of one edge of a peptide beta-strand while blocking the other edge have proven particularly valuable in preventing aggregate formation and in promoting the formation of simple monomeric and dimeric structures. Artificial beta-sheets that present exposed hydrogen-bonding edges can form well-defined hydrogen-bonded dimers. Dimerization occurs readily in chloroform solutions but requires additional hydrophobic interactions to occur in aqueous solution. Interactions among the side chains, as well as hydrogen bonding among the main chains, are important in dimer formation. NMR studies of artificial beta-sheets have elucidated the importance of hydrogen-bonding complementarity, size complementarity, and chiral complementarity in these interactions. These pairing preferences demonstrate sequence selectivity in the molecular recognition between beta-sheets. These studies help illustrate the importance of intermolecular edge-to-edge interactions between beta-sheets in peptides and proteins. Ultimately, these model systems may lead to new ways of controlling beta-sheet interactions and treating diseases in which they are involved.
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Affiliation(s)
- James S Nowick
- Department of Chemistry University of California, Irvine, Irvine, California 92617-4048, USA.
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29
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Amorín M, Castedo L, Granja J. Folding Control in Cyclic Peptides through N-Methylation Pattern Selection: Formation of Antiparallel β-Sheet Dimers, Double Reverse Turns and Supramolecular Helices by 3α,γ Cyclic Peptides. Chemistry 2008; 14:2100-11. [DOI: 10.1002/chem.200701059] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Santiveri C, León E, Rico M, Jiménez M. Context-Dependence of the Contribution of Disulfide Bonds to β-Hairpin Stability. Chemistry 2008; 14:488-99. [DOI: 10.1002/chem.200700845] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Razkin J, Nilsson H, Baltzer L. Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed helix-loop-helix motif peptide. J Am Chem Soc 2007; 129:14752-8. [PMID: 17985898 DOI: 10.1021/ja075478i] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle has been designed to catalyze the hydrolysis of phosphodiesters. The active site on the surface of the folded catalyst is composed of two histidine and four arginine residues, with the capacity to provide general acid, general base, and/or nucleophilic catalysis as well as transition state stabilization. Uridine 3'-2,2,2 trichloroethylphosphate (2) is a mimic of RNA with a leaving group pKa of 12.3. Its hydrolysis is energetically less favorable than that of commonly used model substrates with p-nitrophenyl leaving groups and therefore a more realistic model for the design of catalysts capable of cleaving RNA. The second-order rate constant for the hydrolysis of 2 at pH 7.0 by the polypeptide catalyst was 418 x 10(-6) M-1 s-1, and that of the imidazole catalyzed reaction was 1.66 x 10(-6) M-1 s-1. The pH dependence suggested that catalysis is due to the unprotonated form of a residue with a pKa of around 5.3, and the observed kinetic solvent isotope effect of 1.9 showed that there is significant hydrogen bonding in the transition state, consistent with general acid-base catalysis. The rate constant ratio k2(Pep)/k2(Im) of 252 is probably due to a combination of nucleophilic and general acid-base catalysis, as well as transition state stabilization. Substrate binding was weak since no sign of saturation kinetics was observed for substrate concentrations in the range from 5 to 40 mM. The results provide a platform for the further development of catalysts for RNA cleavage with a potential role in the development of drugs.
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Affiliation(s)
- Jesus Razkin
- Department of Applied Chemistry, Public University of Navarra, 31006 Pamplona, Navarra, Spain.
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32
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Topilina NI, Ermolenkov VV, Higashiya S, Welch JT, Lednev IK. Beta-sheet folding of 11-kDa fibrillogenic polypeptide is completely aggregation driven. Biopolymers 2007; 86:261-4. [PMID: 17377970 DOI: 10.1002/bip.20730] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A de novo polypeptide GH(6)[(GA)(3)GY(GA)(3)GE](8)GAH(6) (YE8) was designed and genetically engineered to form antiparallel beta-strands of GAGAGA repeats. Modulation of pH enables control of solubility, folding, and aggregation of YE8 by control of the overall polypeptide charge, a consequence of the protonation or deprotonation of the glutamic acid and histidine residues. YE8 exhibits all the major properties of a fibrillogenic protein providing an excellent model for detailed study of the fibrillation. At neutral pH, YE8 is soluble in disordered form, yet at pH 3.5 folds into a predominantly beta-sheet conformation that is fibrillogenic. Atomic force microscopy and transmission electron microscopy indicated the formation of fibrillar aggregates on well-defined, hydrophobic surfaces. The beta-sheet folding of YE8 exhibited a lag phase that could be eliminated by seeding or stirring. The strong dependence of lag time on polypeptide concentration established the limiting step in aggregation as initiation of beta-sheet folding.
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Affiliation(s)
- Natalya I Topilina
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
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33
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Riemen AJ, Waters ML. Stabilization of the N-terminal β-hairpin of ubiquitin by a terminal hydrophobic cluster. Biopolymers 2007; 90:394-8. [PMID: 17803200 DOI: 10.1002/bip.20840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Study of model beta-hairpin peptides allows for better understanding of the factors involved in the formation of beta-sheet secondary structure in proteins. It is known that turn sequence, sidechain-sidechain interactions, interstrand hydrogen bonding, and beta-sheet propensity of residues are all important for beta-hairpin stability in aqueous solution. However, interactions of the sidechains of the terminal residues of hairpins are thought to contribute little to overall hairpin stability since these residues are typically frayed. Here, the authors report a stabilizing hydrophobic cluster of residues at the termini of the naturally occurring excised N-terminal beta-hairpin of Ubiquitin that folds autonomously in aqueous solution. Our data show that deletion of Met1 and Val17 from this hairpin destabilized the folded state in both aqueous solution and in aqueous-methanol solutions. These results suggest that interactions of terminal residues which are usually frayed can nonetheless contribute significantly to overall stability of beta-hairpin.
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Affiliation(s)
- Alex J Riemen
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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34
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Schmuck C, Dudaczek J. Ion Pairing Between the Chain Ends Induces Folding of a Flexible Zwitterion in Methanol. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700164] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Woods RJ, Brower JO, Castellanos E, Hashemzadeh M, Khakshoor O, Russu WA, Nowick JS. Cyclic modular beta-sheets. J Am Chem Soc 2007; 129:2548-58. [PMID: 17295482 PMCID: PMC2597679 DOI: 10.1021/ja0667965] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of peptide beta-hairpins is problematic, because folding depends on the amino acid sequence and changes to the sequence can significantly decrease folding. Robust beta-hairpins that can tolerate such changes are attractive tools for studying interactions involving protein beta-sheets and developing inhibitors of these interactions. This paper introduces a new class of peptide models of protein beta-sheets that addresses the problem of separating folding from the sequence. These model beta-sheets are macrocyclic peptides that fold in water to present a pentapeptide beta-strand along one edge; the other edge contains the tripeptide beta-strand mimic Hao [JACS 2000, 122, 7654] and two additional amino acids. The pentapeptide and Hao-containing peptide strands are connected by two delta-linked ornithine (deltaOrn) turns [JACS 2003, 125, 876]. Each deltaOrn turn contains a free alpha-amino group that permits the linking of individual modules to form divalent beta-sheets. These "cyclic modular beta-sheets" are synthesized by standard solid-phase peptide synthesis of a linear precursor followed by solution-phase cyclization. Eight cyclic modular beta-sheets 1a-1h containing sequences based on beta-amyloid and macrophage inflammatory protein 2 were synthesized and characterized by 1H NMR. Linked cyclic modular beta-sheet 2, which contains two modules of 1b, was also synthesized and characterized. 1H NMR studies show downfield alpha-proton chemical shifts, deltaOrn delta-proton magnetic anisotropy, and NOE cross-peaks that establish all compounds but 1c and 1g to be moderately or well folded into a conformation that resembles a beta-sheet. Pulsed-field gradient NMR diffusion experiments show little or no self-association at low (=2 mM) concentrations. Changes to the residues in the Hao-containing strands of 1c and 1g improve folding and show that folding of the structures can be enhanced without altering the sequence of the pentapeptide strand. Well-folded cyclic modular beta-sheets 1a, 1b, and 1f each have a phenylalanine directly across from Hao, suggesting that cyclic modular beta-sheets containing aromatic residues across from Hao are better folded.
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Affiliation(s)
- R. Jeremy Woods
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Justin O. Brower
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Elena Castellanos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Mehrnoosh Hashemzadeh
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Wade A. Russu
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
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36
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Nowick JS. What I have learned by using chemical model systems to study biomolecular structure and interactions. Org Biomol Chem 2006; 4:3869-85. [PMID: 17047863 DOI: 10.1039/b608953b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical model systems provide valuable insights into biomolecular structure and interactions by allowing researchers to simplify, isolate, and manipulate aspects of the complex molecular machinery of living systems. This perspective describes my laboratory's design, synthesis, and study of chemical model systems that fold and self-assemble like proteins and elucidates the insights that have come from studying these systems. Many of these studies have focused on protein beta-sheets, which exhibit fascinating intra- and intermolecular interactions and play important roles in protein folding, aggregation, and molecular recognition.
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Affiliation(s)
- James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
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37
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Imamura H, Chen JZY. Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins. Proteins 2006; 63:555-70. [PMID: 16485280 DOI: 10.1002/prot.20846] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We study the dependence of folding time, nucleation site, and stability of a model beta-hairpin on the location of a cross-strand hydrophobic pair, using a coarse-grained off-lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping-out, middle-out, zipping-in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the beta-turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the beta-turn encourages stability of the entire chain.
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Affiliation(s)
- Hideo Imamura
- Department of Physics, University of Waterloo, Waterloo, Ontario, Canada
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38
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Abstract
Over the past 10 years there has been tremendous success in the area of computational protein design. Protein design software has been used to stabilize proteins, solubilize membrane proteins, design intermolecular interactions, and design new protein structures. A key motivation for these studies is that they test our understanding of protein energetics and structure. De novo design of novel structures is a particularly rigorous test because the protein backbone must be designed in addition to the amino acid side chains. A priori it is not guaranteed that the target backbone is even designable. To address this issue, researchers have developed a variety of methods for generating protein-like scaffolds and for optimizing the protein backbone in conjunction with the amino acid sequence. These protocols have been used to design proteins from scratch and to explore sequence space for naturally occurring protein folds.
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Affiliation(s)
- Glenn L Butterfoss
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA.
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39
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Topilina NI, Higashiya S, Rana N, Ermolenkov VV, Kossow C, Carlsen A, Ngo SC, Wells CC, Eisenbraun ET, Dunn KA, Lednev IK, Geer RE, Kaloyeros AE, Welch JT. Bilayer fibril formation by genetically engineered polypeptides: preparation and characterization. Biomacromolecules 2006; 7:1104-11. [PMID: 16602727 DOI: 10.1021/bm0509016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A de novo, genetically engineered 687 residue polypeptide expressed in E. coli has been found to form highly rectilinear, beta-sheet containing fibrillar structures. Tapping-mode atomic force microscopy, deep-UV Raman spectroscopy, and transmission electron microscopy definitively established the tendency of the fibrils to predominantly display an apparently planar bilayer or ribbon assemblage. The ordered self-assembly of designed, extremely repetitive, high molecular weight peptides is a harbinger of the utility of similar materials in nanoscience and engineering applications.
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Affiliation(s)
- Natalya I Topilina
- Department of Chemistry and College of Nanoscale Science and Engineering, The University at Albany, State University of New York, Albany, New York 12222, USA
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40
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Nikkhah M, Jawad-Alami Z, Demydchuk M, Ribbons D, Paoli M. Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat. ACTA ACUST UNITED AC 2006; 23:185-94. [PMID: 16651025 DOI: 10.1016/j.bioeng.2006.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 01/10/2006] [Accepted: 01/16/2006] [Indexed: 10/24/2022]
Abstract
The ability to design specific amino acid sequences that fold into desired structures is central to engineering novel proteins. Protein design is also a good method to assess our understanding of sequence-structure and structure-function relationships. While beta-sheet structures are important elements of protein architecture, it has traditionally been more difficult to design beta-proteins than alpha-helical proteins. Taking advantage of the tandem repeated sequences that form the structural building blocks in a group of beta-propeller proteins; we have used a consensus design approach to engineer modular and relatively large scaffolds. An idealized WD repeat was designed from a structure-based sequence alignment with a set of structural guidelines. Using a plasmid sequential ligation strategy, artificial concatemeric genes with up to 10 copies of this idealized repeat were then constructed. Corresponding proteins with 4 through to 10 WD repeats were soluble when over-expressed in Escherichia coli. Notably, they were sufficiently stable in vivo surviving attack from endogenous proteases, and maintained a homogeneous, non-aggregated form in vitro. The results show that the beta-propeller scaffold is an attractive platform for future engineering work, particularly in experiments in which directed evolution techniques might improve the stability of the molecules and/or tailor them for a specific function.
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Affiliation(s)
- Maryam Nikkhah
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England, UK
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41
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Huyghues-Despointes BMP, Qu X, Tsai J, Scholtz JM. Terminal ion pairs stabilize the second β-hairpin of the B1 domain of protein G. Proteins 2006; 63:1005-17. [PMID: 16470585 DOI: 10.1002/prot.20916] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The effects of terminal ion pairs on the stability of a beta-hairpin peptide corresponding to the C-terminal residues of the B1 domain of protein G were determined using thermal unfolding as monitored by nuclear magnetic resonance and circular dichroism spectroscopy. Molecular dynamics (MD) simulations were also performed to examine the effect of ion pairs on the structures. Eight peptides were studied including the wild type (G41) and the N-terminal modified sequences that had the first residue deleted (E42), replaced with a Lys (K41), or extended by an additional Gly (G40). Acetylated variants were made to examine the effect of removing the positive N-terminal charge on beta-hairpin stability. The rank in stability determined experimentally is K41 > E42 approximately G41 approximately G40 > Ac-K41 > Ac-E42 approximately Ac-G41 > Ac-G40. The Tm of the K41 peptide is 12 degrees C higher than G41, while the Tm values for the acetylated peptides are less than their unacetylated forms by more than 15 degrees C. NOE cross-peaks between side-chain methylene groups at the N- and C-termini and larger CalphaH shifts compared to random values are seen for K41. The addition of 20% methanol increases the stability in K41 and G41. The MD studies complement these results by showing that the charged N-terminus is important to stability. The type of ion pair observed varies with peptide, and when formed the simulations show that the ion pair can prevent fraying of the beta-strands through electrostatic and hydrophobic contacts. Therefore, introducing favorable electrostatic interactions at the N- and C-termini can substantially enhance beta-hairpin stability and help define the structure.
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42
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Dong SL, Löweneck M, Schrader TE, Schreier WJ, Zinth W, Moroder L, Renner C. A Photocontrolled β-Hairpin Peptide. Chemistry 2006; 12:1114-20. [PMID: 16294349 DOI: 10.1002/chem.200500986] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beta-hairpins constitute the smallest beta-type structures in peptides and proteins. The development of highly stable, yet monomeric beta-hairpins based on the tryptophan zipper motif was therefore a remarkable success [A. G. Cochran, N. J. Skelton, M. A. Starovasnik, Proc. Natl. Acad. Sci USA 2001, 98, 5578-5583]. We have been able to design, synthesize and characterize a hairpin based on this motif which incorporates an azobenzene-based photoswitch, that allows for time-resolved folding studies of beta-structures with unprecedented time resolution. At room temperature the trans-azo isomer exhibits a mostly disordered structure; however, light-induced isomerization to the cis-azo form leads to a predominantly extended and parallel conformation of the two peptide parts, which are linked by the novel photoswitch, [3-(3-aminomethyl)phenylazo]phenylacetic acid (AMPP). While in the original sequence the dipeptide Asn-Gly forms a type I' beta-turn which connects the two strands of the hairpin, this role is adopted by the AMPP chromophore in our photoresponsive beta-hairpin that can apparently act as a beta I'-turn mimetic. The beta-hairpin structure was determined and confirmed by NMR spectroscopy, but the folding process can be monitored by pronounced changes in the CD, IR and fluorescence spectra. Finally, incorporation of the structurally and functionally important beta-hairpin motif into proteins by chemical ligation might allow for the photocontrol of protein structures and/or functions.
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Affiliation(s)
- Shou-Liang Dong
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
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43
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Lins L, Charloteaux B, Heinen C, Thomas A, Brasseur R. "De novo" design of peptides with specific lipid-binding properties. Biophys J 2006; 90:470-9. [PMID: 16275638 PMCID: PMC1367053 DOI: 10.1529/biophysj.105.068213] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 09/13/2005] [Indexed: 11/18/2022] Open
Abstract
In this study, we describe an in silico method to design peptides that can be made of non-natural amino acids and elicit specific membrane-interacting properties. The originality of the method holds in the capacities developed to design peptides from any non-natural amino acids as easily as from natural ones, and to test the structure stability by an angular dynamics rather than the currently-used molecular dynamics. The goal of this study was to design a non-natural tilted peptide. Tilted peptides are short protein fragments able to destabilize lipid membranes and characterized by an asymmetric distribution of hydrophobic residues along their helix structure axis. The method is based on the random generation of peptides and their selection on three main criteria: mean hydrophobicity and the presence of at least one polar residue; tilted insertion at the level of the acyl chains of lipids of a membrane; and conformational stability in that hydrophobic phase. From 10,000,000 randomly-generated peptides, four met all the criteria. One was synthesized and tested for its lipid-destabilizing properties. Biophysical assays showed that the "de novo" peptide made of non-natural amino acids is helical either in solution or into lipids as tested by Fourier transform infrared spectroscopy and is able to induce liposome fusion. These results are in agreement with the calculations and validate the theoretical approach.
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Affiliation(s)
- L Lins
- Centre de Biophysique Moléculaire Numérique, Faculté des Sciences Agronomiques de Gembloux, Gembloux, Belgium
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Santiveri CM, Pantoja-Uceda D, Rico M, Jiménez MA. β-Hairpin formation in aqueous solution and in the presence of trifluoroethanol: A1H and13C nuclear magnetic resonance conformational study of designed peptides. Biopolymers 2005; 79:150-62. [PMID: 16078190 DOI: 10.1002/bip.20345] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid, Spain
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Phillips ST, Piersanti G, Bartlett PA. Quantifying amino acid conformational preferences and side-chain-side-chain interactions in beta-hairpins. Proc Natl Acad Sci U S A 2005; 102:13737-42. [PMID: 16162669 PMCID: PMC1202387 DOI: 10.1073/pnas.0506646102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Indexed: 11/18/2022] Open
Abstract
The intrinsic conformational biases of individual amino acids and their interstrand side-chain-side-chain (SC-SC) interactions both contribute to the stability of beta-sheets. The relative magnitudes of these effects have been difficult to assess in the context of folded proteins, where tertiary contacts complicate the quantitative analysis of local effects. We now report the results of such an analysis in a much simpler system, a short, stabilized beta-hairpin structure where intrastrand (conformational) and interstrand (SC-SC) influences can be distinguished in the absence of competing protein tertiary interactions. A comprehensive comparison of all pairwise combinations of 11 N-terminal and 7 C-terminal amino acids within an 8-residue, @-tide-stabilized [in which @ denotes the 1,2-dihydro-3(6H)-pyridinyl unit] beta-hairpin reveals distinct differences between the various pairings and shows that the intrastrand and interstrand effects are of comparable magnitude in contributing to the stability of the folded forms over the unfolded forms.
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Affiliation(s)
- Scott T Phillips
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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Fotins J, Smithrud DB. Creation and Investigation of Protein-Core Mimetics with Parallel and Antiparallel Aligned Amino Acids. J Org Chem 2005; 70:4452-9. [PMID: 15903324 DOI: 10.1021/jo0479563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mimetic protein cores were created that align a set of l-Phe, d-Phe, or l-Leu residues in a parallel or an antiparallel arrangement in chloroform. Not all cores show a single conformation at room temperature. Stable structures require a synergistic relationship between the H-bonding groups and the residues within the core. The spatial arrangement of the side chains dictates whether a zippered or a crossed pattern of H-bonds is observed for these cores. Variable-temperature (1)H NMR experiments were used to determine the strengths of the H-bonds. The existence of H-bonds was verified through FTIR spectroscopic analysis. Large temperature coefficients exist for some protons of aromatic rings that are held in a T-shaped arrangement. A comparison of these temperature coefficients shows that a more stable core is obtained by combining benzenoid and nitrobenzenoid rings as compared to benzenoid rings. Structures were determined using a combination of 2D NMR analysis and molecular modeling.
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Affiliation(s)
- Juris Fotins
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
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Meier S, Güthe S, Kiefhaber T, Grzesiek S. Foldon, the natural trimerization domain of T4 fibritin, dissociates into a monomeric A-state form containing a stable beta-hairpin: atomic details of trimer dissociation and local beta-hairpin stability from residual dipolar couplings. J Mol Biol 2005; 344:1051-69. [PMID: 15544812 DOI: 10.1016/j.jmb.2004.09.079] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 09/27/2004] [Accepted: 09/27/2004] [Indexed: 11/26/2022]
Abstract
The C-terminal domain of T4 fibritin (foldon) is obligatory for the formation of the fibritin trimer structure and can be used as an artificial trimerization domain. Its native structure consists of a trimeric beta-hairpin propeller. At low pH, the foldon trimer disintegrates into a monomeric (A-state) form that has similar properties as that of an early intermediate of the trimer folding pathway. The formation of this A-state monomer from the trimer, its structure, thermodynamic stability, equilibrium association and folding dynamics have been characterized to atomic detail by modern high-resolution NMR techniques. The foldon A-state monomer forms a beta-hairpin with intact and stable H-bonds that is similar to the monomer in the foldon trimer, but lacks a defined structure in its N and C-terminal parts. Its thermodynamic stability in pure water is comparable to designed hairpins stabilized in alcohol/water mixtures. Details of the thermal unfolding of the foldon A-state have been characterized by chemical shifts and residual dipolar couplings (RDCs) detected in inert, mechanically stretched polyacrylamide gels. At the onset of the thermal transition, uniform relative changes in RDC values indicate a uniform decrease of local N-HN and Calpha-Halpha order parameters for the hairpin strand residues. In contrast, near-turn residues show particular thermal stability in RDC values and hence in local order parameters. This coincides with increased transition temperatures of the beta-turn residues observed by chemical shifts. At high temperatures, the RDCs converge to non-zero average values consistent with predictions from random chain polymer models. Residue-specific deviations above the unfolding transition reveal the persistence of residual order around proline residues, large hydrophobic residues and at the beta-turn.
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Affiliation(s)
- Sebastian Meier
- Division of Structural Biology Biozentrum der Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Abstract
Beside alpha-helices, beta-sheets are the most common secondary structure elements of proteins. In this article, the question of structure and stability of parallel and antiparallel sheets of various lengths is addressed. All data obtained are compared to a selected set of protein structures. In antiparallel beta-sheets, one of the two possible H-bonded structures (containing 14 atoms in the H-bonded pseudoring) is energetically more favored and also more abundant in proteins than the other one (with 10 atoms involved in the pseudoring). Parallel beta-sheets and their subunits are energetically less stable and indeed found to occur more rarely in proteins. Antiparallel hairpins are disfavored compared to beta-sheets formed by sequentially separated strands. Agreement between theory and experimental data indicates that characterization of structural building blocks at an appropriately accurate level of theory is a useful tool to get insight into fundamentals of protein structure.
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Affiliation(s)
- András Perczel
- Department of Organic Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary.
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Pagel K, Vagt T, Koksch B. Directing the secondary structure of polypeptides at will: from helices to amyloids and back again? Org Biomol Chem 2005; 3:3843-50. [PMID: 16239998 DOI: 10.1039/b510098d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation.
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Affiliation(s)
- Kevin Pagel
- Freie Universität Berlin, Institut für Chemie-Organische Chemie, Takustrasse 3, 14195, Berlin, Germany
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Pastor MT, Mora P, Ferrer-Montiel A, Pérez-Payá E. Design of bioactive and structurally well-defined peptides from conformationally restricted libraries. Biopolymers 2004; 76:357-65. [PMID: 15386263 DOI: 10.1002/bip.20142] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Libraries of peptides and proteins can be categorized according to the function of their origin in gene- and synthetic-based libraries. Both kinds of libraries have the potential to generate the same grade of molecular diversity, although the limits imposed by the synthetic methods have been lately a matter of discussion. However, the use of synthetic strategies allows incorporation of non-natural amino acids. The development of conformationally restricted synthetic peptide libraries can be considered as a point of convergence of the two methodologies. In these libraries the diversity is grafted into scaffolds that are defined by stable secondary structural motifs, and the deconvolution protocols can be directed towards the identification of biologically active molecules and the analysis of determinants of folding of protein domains.
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Affiliation(s)
- M Teresa Pastor
- Department de Bioquímica i Biologia Molecular, Universitat de València, E-46100 Burjassot, València, Spain
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