1
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Zhang S. Discovery of the first self-assembling peptide, study of peptide dynamic behaviors, and G protein-coupled receptors using an Aviv circular dichroism spectropolarimeter. Biopolymers 2019; 109:e23235. [PMID: 30269347 DOI: 10.1002/bip.23235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 11/10/2022]
Abstract
Circular dichroism (CD) spectroscopy is a useful technique to study the structure and dynamics of peptides, proteins and nucleic acids. CD is particularly useful because sample volumes may be as low as 50 μL, it provides high precision and sensitivity, and it achieves a good signal to noise ratio. CD characterizes molecular conformational changes in real time by finely controlling temperature, pH, and titrating urea and guanidine·HCl which is necessary for studying protein folding. Although CD does not provide detailed structure at the atomic level, it provides a global structural framework. Researchers use CD to observe molecular phenomena, namely how macromolecules unfold/refold and their overall self-assembly/disassembly. Using CD to monitor a peptide structure, I serendipitously discovered the self-assembling peptide EAK16 from yeast protein Zuotin. This unusual peptide formed a new type of nanofiber scaffold hydrogel material. The discovery in 1990 opened a new field in the design and study of numerous self-assembling peptides, thereby launching the area of peptide nanobiotechnology. In this review, I reflect on my personal discoveries of several self-assembling peptides, investigations into the dynamic behaviors of peptides, as well as the impact of the work on society. I also describe studies of natural membrane proteins and engineered membrane proteins using CD. Furthermore, I enjoyed numerous and close interactions with Jack Aviv since 1997. He generously supported 10 high impact workshops (Crete and Mikonos) and meetings in various countries around the world that left fond memories of many young researches who later became leading scientists in their respective fields.
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Affiliation(s)
- Shuguang Zhang
- Center for Bits and Atoms E15-401, Massachusetts Institute of Technology, Cambridge, Massachusetts
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2
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Luber S. Solvent Effects in Calculated Vibrational Raman Optical Activity Spectra of α-Helices. J Phys Chem A 2013; 117:2760-70. [DOI: 10.1021/jp400105u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Luber
- University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
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3
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Park M, Wetzler M, Jardetzky TS, Barron AE. A readily applicable strategy to convert peptides to peptoid-based therapeutics. PLoS One 2013; 8:e58874. [PMID: 23555603 PMCID: PMC3605428 DOI: 10.1371/journal.pone.0058874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/07/2013] [Indexed: 01/23/2023] Open
Abstract
Incorporation of unnatural amino acids and peptidomimetic residues into therapeutic peptides is highly efficacious and commonly employed, but generally requires laborious trial-and-error approaches. Previously, we demonstrated that C20 peptide has the potential to be a potential antiviral agent. Herein we report our attempt to improve the biological properties of this peptide by introducing peptidomimetics. Through combined alanine, proline, and sarcosine scans coupled with a competitive fluorescence polarization assay developed for identifying antiviral peptides, we enabled to pinpoint peptoid-tolerant peptide residues within C20 peptide. The synergistic benefits of combining these (and other) commonly employed methods could lead to a easily applicable strategy for designing and refining therapeutically-attractive peptidomimetics.
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Affiliation(s)
- Minyoung Park
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Modi Wetzler
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, California, United States of America
| | - Theodore S. Jardetzky
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Annelise E. Barron
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
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4
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Sánchez-Martín MJ, Cruz A, Busquets MA, Haro I, Alsina MA, Pujol M. Physicochemical characterization of GBV-C E1 peptides as potential inhibitors of HIV-1 fusion peptide: Interaction with model membranes. Int J Pharm 2012; 436:593-601. [DOI: 10.1016/j.ijpharm.2012.07.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 11/29/2022]
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5
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Hatakeyama Y, Sawada T, Kawano M, Fujita M. Conformational preferences of short peptide fragments. Angew Chem Int Ed Engl 2010; 48:8695-8. [PMID: 19816897 DOI: 10.1002/anie.200903563] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yoshiyuki Hatakeyama
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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6
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Hatakeyama Y, Sawada T, Kawano M, Fujita M. Conformational Preferences of Short Peptide Fragments. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Diana D, Ziaco B, Colombo G, Scarabelli G, Romanelli A, Pedone C, Fattorusso R, D'Andrea L. Structural Determinants of the Unusual Helix Stability of a De Novo Engineered Vascular Endothelial Growth Factor (VEGF) Mimicking Peptide. Chemistry 2008; 14:4164-6. [DOI: 10.1002/chem.200800180] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Jin HX, Wu TX, Jiang YJ, Zou JW, Zhuang SL, Zhang N, Mao X, Yu QS. Functional role of three water molecules buried within catalytic subunit of cyclic 3′,5′-adenosine monophosphate-dependent protein kinase. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Tashiro S, Tominaga M, Yamaguchi Y, Kato K, Fujita M. Folding a De Novo Designed Peptide into an α-Helix through Hydrophobic Binding by a Bowl-Shaped Host. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502802] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Tashiro S, Tominaga M, Yamaguchi Y, Kato K, Fujita M. Folding a De Novo Designed Peptide into an α-Helix through Hydrophobic Binding by a Bowl-Shaped Host. Angew Chem Int Ed Engl 2006; 45:241-4. [PMID: 16312001 DOI: 10.1002/anie.200502802] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shohei Tashiro
- Department of Applied Chemistry, School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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11
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McColl IH, Blanch EW, Hecht L, Barron LD. A Study of α-Helix Hydration in Polypeptides, Proteins, and Viruses Using Vibrational Raman Optical Activity. J Am Chem Soc 2004; 126:8181-8. [PMID: 15225059 DOI: 10.1021/ja048991u] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A vibrational Raman optical activity (ROA) study, supplemented by protein X-ray crystal structure data, of alpha-helices in polypeptides, proteins, and viruses has suggested that ROA bands in the extended amide III spectral region may be used to distinguish between two types of right-handed alpha-helix. One type, associated with a positive ROA band at approximately 1300 cm(-1), dominates in hydrophobic environments and appears to be unhydrated; the other, associated with a positive ROA band at approximately 1340 cm(-1), dominates in hydrophilic environments and appears to be hydrated. Evidence is presented to support the hypothesis that unhydrated alpha-helix corresponds to the canonical conformation alpha(c) and hydrated alpha-helix to a more open conformation alpha(o) stabilized by hydrogen bonding of a water molecule or a hydrophilic side chain to the peptide carbonyl. Alpha-helical poly(L-lysine) and poly(L-ornithine) in aqueous solution and poly(L-alanine) in dichloracetic acid display both bands, but alpha-helical poly(l-glutamic acid) in aqueous solution and poly(gamma-benzyl L-glutamate) in CHCl(3) display only the approximately 1340 cm(-1) band and so may exist purely as alpha(o) due to enhanced stabilization of this conformation by particular side chain characteristics. The ROA spectrum of poly(beta-benzyl L-aspartate) in CHCl(3) reveals that it exists in a single left-handed alpha-helical state more analogous to alpha(o) than to alpha(c).
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Affiliation(s)
- Iain H McColl
- Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
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12
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Roccatano D, Di Nola A, Amadei A. A Theoretical Model for the Folding/Unfolding Thermodynamics of Single-Domain Proteins, Based on the Quasi-Gaussian Entropy Theory. J Phys Chem B 2004. [DOI: 10.1021/jp037591a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Danilo Roccatano
- School of Engineering and Science, International University Bremen, Campus Ring 1, D-28725 Bremen, Germany, Dipartimento di Chimica Università di Roma “La Sapienza” P.le A. Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze e Tecnologie Chimiche Università di Roma “Tor Vergata”, via della Ricerca Scientifica 1, I-00133 Roma, Italy
| | - A. Di Nola
- School of Engineering and Science, International University Bremen, Campus Ring 1, D-28725 Bremen, Germany, Dipartimento di Chimica Università di Roma “La Sapienza” P.le A. Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze e Tecnologie Chimiche Università di Roma “Tor Vergata”, via della Ricerca Scientifica 1, I-00133 Roma, Italy
| | - Andrea Amadei
- School of Engineering and Science, International University Bremen, Campus Ring 1, D-28725 Bremen, Germany, Dipartimento di Chimica Università di Roma “La Sapienza” P.le A. Moro 5, 00185 Roma, Italy, and Dipartimento di Scienze e Tecnologie Chimiche Università di Roma “Tor Vergata”, via della Ricerca Scientifica 1, I-00133 Roma, Italy
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13
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Santiveri CM, Santoro J, Rico M, Jiménez MA. Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial. Protein Sci 2004; 13:1134-47. [PMID: 15044739 PMCID: PMC2280049 DOI: 10.1110/ps.03520704] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/15/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
We have recently reported on the design of a 20-residue peptide able to form a significant population of a three-stranded up-and-down antiparallel beta-sheet in aqueous solution. To improve our beta-sheet model in terms of the folded population, we have modified the sequences of the two 2-residue turns by introducing the segment DPro-Gly, a sequence shown to lead to more rigid type II' beta-turns. The analysis of several NMR parameters, NOE data, as well as Deltadelta(CalphaH), DeltadeltaC(beta), and Deltadelta(Cbeta) values, demonstrates that the new peptide forms a beta-sheet structure in aqueous solution more stable than the original one, whereas the substitution of the DPro residues by LPro leads to a random coil peptide. This agrees with previous results on beta-hairpin-forming peptides showing the essential role of the turn sequence for beta-hairpin folding. The well-defined beta-sheet motif calculated for the new designed peptide (pair-wise RMSD for backbone atoms is 0.5 +/- 0.1 A) displays a high degree of twist. This twist likely contributes to stability, as a more hydrophobic surface is buried in the twisted beta-sheet than in a flatter one. The twist observed in the up-and-down antiparallel beta-sheet motifs of most proteins is less pronounced than in our designed peptide, except for the WW domains. The additional hydrophobic surface burial provided by beta-sheet twisting relative to a "flat" beta-sheet is probably more important for structure stability in peptides and small proteins like the WW domains than in larger proteins for which there exists a significant contribution to stability arising from their extensive hydrophobic cores.
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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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14
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Read MJ, Burkett SL. Asymmetric -helicity loss within a peptide adsorbed onto charged colloidal substrates. J Colloid Interface Sci 2003; 261:255-63. [PMID: 16256530 DOI: 10.1016/s0021-9797(03)00092-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2002] [Accepted: 01/16/2003] [Indexed: 10/27/2022]
Abstract
A combination of circular dichroism and solution 1H NMR spectroscopy provides a localized description of the distribution of alpha -helical structure within the capped peptide DDDDAAAAARRRR (4DAR5) in aqueous solution and adsorbed onto anionic and cationic colloidal substrates. The adsorption-induced conformational changes are different from those observed upon heating 4DAR5 in solution, in which case the alanine segment remains largely alpha -helical and the transition to a coil structure propagates from the termini. Adsorption is driven by electrostatic complementarity, which places the charged peptide segment adjacent to the substrate of opposite charge. A similar pattern of alpha -helicity loss is observed whether the peptide is adsorbed onto anionic or cationic colloidal silica, despite inverse orientations; significant alpha -helicity loss occurs within the central alanine segment and the terminal arginine segment, whereas alpha -helicity is retained in the aspartate segment. This pattern of adsorption-induced conformational change illustrates the complex and subtle balance among the intramolecular and intermolecular factors that influence the conformations of adsorbed peptides and proteins.
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Affiliation(s)
- Michael J Read
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Santiveri CM, Rico M, Jiménez MA, Pastor MT, Pérez-Payá E. Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 61:177-88. [PMID: 12605603 DOI: 10.1034/j.1399-3011.2003.00045.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In a previous study we designed a 20-residue peptide able to adopt a significant population of a three-stranded antiparallel beta-sheet in aqueous solution (de Alba et al. [1999]Protein Sci.8, 854-865). In order to better understand the factors contributing to beta-sheet folding and stability we designed and prepared nine variants of the parent peptide by substituting residues at selected positions in its strands. The ability of these peptides to form the target motif was assessed on the basis of NMR parameters, in particular NOE data and 13Calpha conformational shifts. The populations of the target beta-sheet motif were lower in the variants than in the parent peptide. Comparative analysis of the conformational behavior of the peptides showed that, as expected, strand residues with low intrinsic beta-sheet propensities greatly disfavor beta-sheet folding and that, as already found in other beta-sheet models, specific cross-strand side chain-side chain interactions contribute to beta-sheet stability. More interestingly, the performed analysis indicated that the destabilization effect of the unfavorable strand residues depends on their location at inner or edge strands, being larger at the latter. Moreover, in all the cases examined, favorable cross-strand side chain-side chain interactions were not strong enough to counterbalance the disfavoring effect of a poor beta-sheet-forming residue, such as Gly.
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Affiliation(s)
- C M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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16
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Colombo G, De Mori GMS, Roccatano D. Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study. Protein Sci 2003; 12:538-50. [PMID: 12592024 PMCID: PMC2312445 DOI: 10.1110/ps.0227203] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2002] [Revised: 11/11/2002] [Accepted: 12/02/2002] [Indexed: 10/27/2022]
Abstract
We investigated the structural determinants of the stability of a designed beta-hairpin containing a natural hydrophobic cluster from the protein GB1 and a D-Pro-Gly turn forming sequence. The results of our simulations shed light on the factors leading to an ordered secondary structure in a model peptide: in particular, the importance of the so-called diagonal interactions in forming a stable hydrophobic nucleus in the beta-hairpin, together with the more obvious lateral interactions, is examined. With the use of long timescale MD simulations in explicit water, we show the role of diagonal interactions in driving the peptide to the correct folded structure (formation of the hydrophobic core with Trp 2, Tyr 4, and Phe 9 in the first stages of refolding) and in keeping it in the ensemble of folded conformations. The combination of the stabilizing effects of the D-Pro-Gly turn sequence and of the hydrophobic nucleus formation thus favors the attainment of an ordered secondary structure compatible with the one determined experimentally. Moreover, our data underline the importance of the juxtapositions of the side chains of amino acids not directly facing each other in the three-dimensional structure. The combination of these interactions forces the peptide to sample a nonrandom portion of the conformational space, as can be seen in the rapid collapse to an ordered structure in the refolding simulation, and shows that the unfolded state can be closely correlated to the folded ensemble of structures, at least in the case of small model peptides.
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Affiliation(s)
- Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milano, Italy.
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17
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Bour P, Kubelka J, Keiderling TA. Ab initio quantum mechanical models of peptide helices and their vibrational spectra. Biopolymers 2002; 65:45-59. [PMID: 12209472 DOI: 10.1002/bip.10224] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
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18
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Venyaminov SY, Hedstrom JF, Prendergast FG. Analysis of the segmental stability of helical peptides by isotope-edited infrared spectroscopy. Proteins 2001; 45:81-9. [PMID: 11536363 DOI: 10.1002/prot.1126] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Isotope-edited infrared spectroscopy has the ability to probe the segmental properties of long biopolymers. In this work, we have compared the infrared spectra of a model helical peptide ((12)C) Ac-W-(E-A-A-A-R)(6)-A-NH(2), described originally by Merutka et al. (Biochemistry 1991;30:4245-4248) and three derivatives that are (13)C labeled at the backbone carbonyl of alanines. The locations of six isotopically labeled alanines are at the N-terminal, C-terminal, and the middle two repeating units of the peptide. Variation in temperature from 1 degrees to 91 degrees C transformed the peptides from predominantly helical to predominantly disordered state. Amplitude and position of the infrared amide I' absorption bands from (12)C- and (13)C-labeled segments provided information about the helical content. Temperature dependence of infrared spectra was used to estimate segmental stability. As a control measure of overall peptide stability and helicity (independent of labeling), the temperature dependence of circular dichroism spectra in the far-UV range at identical conditions (temperature and solvent) as infrared spectra was measured. The results indicate that the central quarter of the 32 amino acids helix has the maximal helicity and stability. The midpoint of the melting curve of the central quarter of the helix is 5.4 +/- 0.8 degrees C higher than that of the termini. The N-terminal third of the helix is more helical and is 2.0 +/- 1.4 degrees C more stable than the C-terminus.
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Affiliation(s)
- S Y Venyaminov
- Department of Biochemistry and Molecular Biology, Mayo Foundation Rochester, Minnesota 55905, USA.
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19
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Alexander McNamara LM, Andrews MJ, Mitzel F, Siligardi G, Tabor AB. Peptides constrained by an aliphatic linkage between two C(alpha) sites: design, synthesis, and unexpected conformational properties of an i,(i + 4)-linked peptide. J Org Chem 2001; 66:4585-94. [PMID: 11421778 DOI: 10.1021/jo015508e] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel route for the synthesis of cyclic peptides constrained by an aliphatic bridge between two C(alpha)sites, using a triply orthogonal protecting group strategy, is described. The synthesis of the orthogonally protected bis-amino acid 1, via an enantioselective route utilizing the Schöllkopf and Evans methodologies, is first described. This is then incorporated into a short, alanine-rich peptide 13, using a novel triply orthogonal protecting group strategy to couple first one, then the other, amino acid moiety in such a way that an aliphatic bridge is formed between the i and i + 4 positions. Unexpectedly, the resulting constrained peptide does not adopt a helical conformation: instead, it is shown by CD at low temperature to adopt a left-handed type II beta-turn conformation in aqueous media and a right-handed type I beta-turn conformation in TFE.
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Affiliation(s)
- L M Alexander McNamara
- Department of Chemistry, University College London, Christoper Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, U.K
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20
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Barron LD, Hecht L, Blanch EW, Bell AF. Solution structure and dynamics of biomolecules from Raman optical activity. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2000; 73:1-49. [PMID: 10781828 DOI: 10.1016/s0079-6107(99)00017-6] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Raman optical activity (ROA) measures vibrational optical activity by means of a small difference in the intensity of Raman scattering from chiral molecules in right and left circularly polarized incident laser light. The ROA spectra of a wide range of biomolecules in aqueous solution can now be measured routinely. Because of its sensitivity to the chiral elements of biomolecular structure, ROA provides new information about solution structure and dynamics complementary to that supplied by conventional spectroscopic techniques. This article provides a brief introduction to the theory and practice of ROA spectroscopy followed by a review of recent ROA results on polypeptides, proteins, carbohydrates, nucleic acids and viruses which illustrate how new insight into current problems of structure, folding and function may be obtained from ROA studies.
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Affiliation(s)
- L D Barron
- Chemistry Department, University of Glasgow, Glasgow, UK.
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21
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Abstract
Several de novo designed ionic peptides that are able to undergo conformational change under the influence of temperature and pH were studied. These peptides have two distinct surfaces with regular repeats of alternating hydrophilic and hydrophobic side chains. This permits extensive ionic and hydrophobic interactions resulting in the formation of stable beta-sheet assemblies. The other defining characteristic of this type of peptide is a cluster of negatively charged aspartic or glutamic acid residues located toward the N-terminus and positively charged arginine or lysine residues located toward the C-terminus. This arrangement of charge balances the alpha-helical dipole moment (C --> N), resulting in a strong tendency to form stable alpha-helices as well. Therefore, these peptides can form both stable alpha-helices and beta-sheets. They are also able to undergo abrupt structural transformations between these structures induced by temperature and pH changes. The amino acid sequence of these peptides permits both stable beta-sheet and alpha-helix formation, resulting in a balance between these two forms as governed by the environment. Some segments in proteins may also undergo conformational changes in response to environmental changes. Analyzing the plasticity and dynamics of this type of peptide may provide insight into amyloid formation. Since these peptides have dynamic secondary structure, they will serve to refine our general understanding of protein structure.
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Affiliation(s)
- M Altman
- Center for Biomedical Engineering & Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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22
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Grell D, Richardson JS, Richardson DC, Mutter M. SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. J Mol Graph Model 2000; 18:290-8, 309-10. [PMID: 11021545 DOI: 10.1016/s1093-3263(00)00049-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.
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Affiliation(s)
- D Grell
- Institute of Organic Chemistry, University of Lausanne, Switzerland
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Blanch EW, Bell AF, Hecht L, Day LA, Barron LD. Raman optical activity of filamentous bacteriophages: hydration of alpha-helices. J Mol Biol 1999; 290:1-7. [PMID: 10388553 DOI: 10.1006/jmbi.1999.2871] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the first observations of vibrational Raman optical activity (ROA) on intact viruses. Specifically, ROA spectra of the filamentous bacteriophages Pf1, M13 and IKe in aqueous solution were measured in the range approximately 600-1800 cm-1. On account of its ability to probe directly the chiral elements of biomolecular structure, ROA has provided a new perspective on the solution structures of these well-studied systems. The ROA spectra of all three are dominated by signatures of helical elements in the major coat proteins, as expected from pre-existing data. The helical elements generate strong sharp positive ROA bands at approximately 1300 and 1342 cm-1in H2O solution, but in2H2O solution the approximately 1342 cm-1bands disappear completely. The spectra are similar to those of polypeptides under conditions that produce alpha-helical conformations. Our present results, together with results from other studies, suggest that the positive approximately 1342 cm-1ROA bands are generated by a highly hydrated form of alpha-helix, and that the positive approximately 1300 cm-1bands originate in alpha-helix in a more hydrophobic environment. The presence of significant amounts of highly hydrated helical sequences accords with the known flexibility of these viruses. Differences of spectral detail for Pf1, M13 and IKe demonstrate that ROA is sensitive to subtle variations of conformation and hydration within the major coat proteins, with M13 and IKe possibly containing more non-helical structure than Pf1. The ROA spectra of Pf1 at temperatures above and below that at which a structural transition is known to occur (approximately 10 degrees C) reveal little difference in the protein conformation between the two forms, but there are indications of changes in DNA structure.
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Affiliation(s)
- E W Blanch
- Chemistry Department, University of Glasgow, Glasgow, G12 8QQ, UK
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Wan WY, Milner-White EJ. A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations. J Mol Biol 1999; 286:1651-62. [PMID: 10064721 DOI: 10.1006/jmbi.1999.2551] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Side-chain hydroxyl residues in protein crystal structures often form hydrogen bonds with main-chain atoms. The most common bond arrangement is a four to five residue motif in which a serine or threonine is the first residue forming two characteristic hydrogen bonds to residues ahead of it in sequence. We call them ST-motifs, by analogy with the term Asx-motif we suggested for the related motifs with aspartate and asparagine residues. ST-motifs are common, there being just under one and a half in a typical protein subunit. Asx-motifs are even more common, such that 9 % of the residues of an average protein consist of Asx or ST-motifs. Of the ST-motifs, three-quarters are at helical N termini, and the rest occur by themselves or in conjunction with beta-bulge loops. A third of all alpha-helices have either ST-motifs or Asx-motifs at their N termini. Previous work has emphasised the occurrence of the capping box at alpha-helical N termini, but the capping box occurs in only 5 % of alpha-helical N termini; also, we point out that it can be regarded as a subset of the ST-motif (or, occasionally, of the Asx-motif). By comparing related sequences, the rates which amino acid residues at the first position of ST or Asx-motifs interchange during evolution are examined. Serine <==> threonine, and aspartate <==> asparagine, interchange is rapid; inter-pair exchange is slower, but much faster than exchange with other amino acid residues. This is consistent with the general similarity of ST-motifs and Asx-motifs combined with some subtle structural differences between them that are described.
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Affiliation(s)
- W Y Wan
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Wan WY, Milner-White EJ. A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations. J Mol Biol 1999; 286:1633-49. [PMID: 10064720 DOI: 10.1006/jmbi.1999.2552] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Examination of the ways side-chain carboxylate and amide groups in high-resolution protein crystal structures form hydrogen bonds with main-chain atoms reveals that the most common category is a two-hydrogen-bond four to five residue motif with an aspartate or asparagine (Asx) at the first residue, for which we propose the name Asx-motif. Similar motifs with glutamate or glutamine residues at that position are rare. Asx-motifs occur typically as (1) a common feature of the N termini of alpha-helices called the Asx N-cap motif; (2) an independent motif, usually a beta-turn with an appropriately hydrogen-bonded Asx as the first residue; and (3) a motif incorporated in a beta-bulge loop. Asx-motifs are common, there being just under two-and-a-half in an average-sized protein subunit; of these, about 55 % are Asx N-cap motifs. Because they occur often in many situations, it seems that these motifs have an inherent propensity to form on their own rather than just being a feature stabilised at the end of a helix. Asx-motifs also occur in functionally interesting situations in aspartyl proteases, citrate synthase, EF hands, haemoglobins, lipocalins, glutathione reductase and the alpha/beta hydrolases.
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Affiliation(s)
- W Y Wan
- Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Steinmetz MO, Stock A, Schulthess T, Landwehr R, Lustig A, Faix J, Gerisch G, Aebi U, Kammerer RA. A distinct 14 residue site triggers coiled-coil formation in cortexillin I. EMBO J 1998; 17:1883-91. [PMID: 9524112 PMCID: PMC1170535 DOI: 10.1093/emboj/17.7.1883] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have investigated the process of the assembly of the Dictyostelium discoideum cortexillin I oligomerization domain (Ir) into a tightly packed, two-stranded, parallel coiled-coil structure using a variety of recombinant polypeptide chain fragments. The structures of these Ir fragments were analyzed by circular dichroism spectroscopy, analytical ultracentrifugation and electron microscopy. Deletion mapping identified a distinct 14 residue site within the Ir coiled coil, Arg311-Asp324, which was absolutely necessary for dimer formation, indicating that heptad repeats alone are not sufficient for stable coiled-coil formation. Moreover, deletion of the six N-terminal heptad repeats of Ir led to the formation of a four- rather than a two-helix structure, suggesting that the full-length cortexillin I coiled-coil domain behaves as a cooperative folding unit. Most interestingly, a 16 residue peptide containing the distinct coiled-coil 'trigger' site Arg311-Asp324 yielded approximately 30% helix formation as monomer, in aqueous solution. pH titration and NaCl screening experiments revealed that the peptide's helicity depends strongly on pH and ionic strength, indicating that electrostatic interactions by charged side chains within the peptide are critical in stabilizing its monomer helix. Taken together, these findings demonstrate that Arg311-Asp324 behaves as an autonomous helical folding unit and that this distinct Ir segment controls the process of coiled-coil formation of cortexillin I.
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Affiliation(s)
- M O Steinmetz
- M.E.Müller Institute for Microscopy, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Wilson G, Hecht L, Barron LD. Residual structure in unfolded proteins revealed by Raman optical activity. Biochemistry 1996; 35:12518-25. [PMID: 8823188 DOI: 10.1021/bi961314v] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Because of its ability to probe directly the chiral elements of the peptide backbone, together with the very short time scale of the scattering process, vibrational Raman optical activity (ROA) can provide new information on structure in non-native states of proteins. Here we report ROA studies of hen egg white lysozyme and bovine ribonuclease A in unfolded denatured states, prepared by reducing all the disulfide bonds. ROA spectra of unfolded lysozyme at 45, 20, and 2 degrees C, and of unfolded ribonuclease A at 35 and 20 degrees C, are presented and discussed. At 45 and 20 degrees C, unfolded lysozyme appears to contain very little extended secondary structure, but at 2 degrees C there could be roughly 20% of the native amount of alpha-helix present but little beta-sheet. Unfolded ribonuclease A, on the other hand, appears to contain roughly 50% of its native-like secondary structure, including both alpha-helix and beta-sheet, at 20 degrees C; similar secondary structure persists at 35 degrees C, but the amount is reduced. The most striking result is the observation of three sharp ROA bands in the extended amide III region, originating in coupled C alpha-H and N-H deformations, which might monitor directly the dominant intrinsic propensities for residues to adopt particular phi, psi angles, averaged over the different amino acids in the mobile heteropolypeptide. Specifically, positive bands at approximately 1300 and 1314 cm-1 appear to monitor propensities for alpha-helix and beta-structure, respectively, and a negative band at approximately 1237 cm-1 appears to monitor that for the poly(L-proline) II helix. These signals are generated by individual residues clustering in the most favorable regions of the Ramachandran plot and are present even in the absence of signals from the corresponding extended secondary structures. At 45 degrees C, the 1300 and 1314 cm-1 ROA bands of unfolded lysozyme coalesce into a single sharp band from which an analysis similar to that used for exchange effects in NMR suggests a rate of approximately 2.6 x 10(12) s-1 for interconversion between the individual residue conformations at this temperature.
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Affiliation(s)
- G Wilson
- Chemistry Department, University, Glasgow, U.K
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