1
|
Bertran A, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Determining and controlling conformational information from orientationally selective light-induced triplet-triplet electron resonance spectroscopy for a set of bis-porphyrin rulers. Phys Chem Chem Phys 2024; 26:2589-2602. [PMID: 38170870 PMCID: PMC10793979 DOI: 10.1039/d3cp03454b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 01/05/2024]
Abstract
We recently reported a new technique, light-induced triplet-triplet electron resonance (LITTER) spectroscopy, which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin-porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron-electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells.
Collapse
Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Alice M Bowen
- The National Research Facility for Electron Paramagnetic Resonance, Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| |
Collapse
|
2
|
Pal S, Banerjee S, Kumar A, Prabhakaran EN. H-Bond Surrogate-Stabilized Shortest Single-Turn α-Helices: sp 2 Constraints and Residue Preferences for the Highest α-Helicities. ACS OMEGA 2020; 5:13902-13912. [PMID: 32566857 PMCID: PMC7301546 DOI: 10.1021/acsomega.0c01277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 05/08/2023]
Abstract
Short α-helical sequences of proteins fail to maintain their native conformation when taken out of their protein context. Several covalent constraints have been designed, including the covalent H-bond surrogate (HBS)-where a peptide backbone i + 4 → i H-bond is replaced by a covalent surrogate-to nucleate α-helix in short sequences (>7 < 15 amino acids). But constraining the shortest sequences (four amino acids) into a single α-helical turn is still a significant challenge. Here, we introduce an HBS model that can be placed in unstructured tetrapeptides without excising any of its residues, and that biases them predominantly into remarkably stable single α-helical turns in varying solvents, pH values, and temperatures. Circular dichroism (CD), Fourier transform infrared (FT-IR) absorption, one-dimensional (1D)-NMR, two-dimensional (2D)-NMR spectral and computational analyses of the HBS-constrained tetrapeptide analogues reveal that (a) the number of sp2 atoms in the HBS-constrained backbone influences their predominance and rigidity in the α-helical conformation; and (b) residue preferences at the unnatural HBS-constrained positions influence their α-helicities, with Moc[GFA]G-OMe (1a) showing the highest known α-helicity (θn→π*MRE ∼-25.3 × 103 deg cm2 dmol-1 at 228 nm) for a single α-helical turn. Current findings benefit chemical biological applications desiring predictable access to single α-helical turns in tetrapeptides.
Collapse
|
3
|
Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| |
Collapse
|
4
|
Chen J, Kohler B. Base stacking in adenosine dimers revealed by femtosecond transient absorption spectroscopy. J Am Chem Soc 2014; 136:6362-72. [PMID: 24735123 DOI: 10.1021/ja501342b] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Excitons formed in DNA by UV absorption decay via poorly understood pathways that can culminate in mutagenic photoproducts. In order to gain insight into how base stacking influences UV excited states in DNA, five dinucleosides composed of adenosine or 2'-deoxyadenosine units joined by flexible linkers were studied by femtosecond transient absorption spectroscopy. In aqueous solution, transient absorption signals recorded at pump and probe wavelengths of 267 and 250 nm, respectively, show that UV absorption produces excimer states in all dimers that decay orders of magnitude more slowly than excitations in a single adenine nucleotide. Adding methanol as a cosolvent disrupts π-π stacking of the adenine moieties and causes the excimer states in all five dinucleosides to vanish for a methanol concentration of 80% by volume. These observations confirm that base stacking is an essential requirement for the slow decay channel seen in these and other DNA model compounds. This channel appears to be insensitive to the precise stacking conformation at the instant of photon absorption as long as the bases are cofacially stacked. Notably, circular dichroism (CD) spectra of several of the dinucleosides are weak and monomer-like and lack the exciton coupling that has been emphasized in the past as an indicator of base-stacked structure. For these dimers, the coupled transition dipole moments of the two adenines are proposed to adopt left- and right-handed arrangements upon stacking with roughly equal probability. Although the mechanism behind slow nonradiative decay in DNA is still uncertain, these results show that the signature of these states in transient absorption experiments can be a more reliable diagnostic of base stacking than the occurrence of exciton-coupled CD signals. These observations also draw attention to the important role the backbone plays in producing structures with axial (helical) chirality.
Collapse
Affiliation(s)
- Jinquan Chen
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717-3400, United States
| | | |
Collapse
|
5
|
Onoda A, Igarashi M, Naganawa S, Sasaki K, Ariyasu S, Yamamura T. Circular Dichroism of Neutral Zinc Porphyrin–Oligonucleotide Conjugates Modified with Flexible Linker. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1280] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
6
|
Abstract
Molecular systems containing two or more interacting porphyrins show remarkable spectroscopic features that allow for a very sensitive detection of conformational changes on the microscale level by different methods, such as fluorescence and electronic circular dichroism (ECD). Covalent porphyrin-DNA assemblies can provide a CD profile (exciton couplet) within the porphyrin Soret band region which is very diagnostic for DNA conformational changes. Additionally, covalently linked porphyrins have been shown to function as DNA molecular caps and to stabilize the non-self-complementary non-Watson-Crick guanine-adenine DNA sequence via their strong π-π stacking.
Collapse
|
7
|
Guryanov I, Moretto A, Campestrini S, Broxterman QB, Kaptein B, Peggion C, Formaggio F, Toniolo C. Turn and helical peptide spacers: Combined distance and angular dependencies in the exciton-coupled circular dichroism of intramolecularly interacting bis-porphyrins. Biopolymers 2006; 82:482-90. [PMID: 16518849 DOI: 10.1002/bip.20500] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In a previous study we examined by the exciton-coupled circular dichroic method the distance effect generated by three-rigid-turn and helical-peptide spacers. In this connection porphyrins were confirmed to be excellent reporter chromophores. In the present investigation we have completed this research by expanding the original analysis to the assessment of the combined role of the chromophore distance and orientation with use of the same porphyrin derivatives and additional four analogous spacers of different main-chain lengths. We find that not only the intramolecular separation of the chromophores, but the angular dependence between the directions of their effective transition moments as well, are responsible for the onset and modulation of the intensity of the exciton-coupling phenomenon of the porphyrin Soret band.
Collapse
Affiliation(s)
- Ivan Guryanov
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Balaz M, Holmes AE, Benedetti M, Proni G, Berova N. Porphyrin substituted phosphoramidites: new building blocks for porphyrin-oligonucleotide syntheses. Bioorg Med Chem 2005; 13:2413-21. [PMID: 15755643 DOI: 10.1016/j.bmc.2005.01.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2004] [Revised: 01/22/2005] [Accepted: 01/25/2005] [Indexed: 10/25/2022]
Abstract
Thymidine phosphoramidites containing trispyridylphenyl and tetraphenylporphyrin chromophores attached via a short amide linker in the 3'-position have been synthesized and used as building blocks in solid-phase synthesis of self-complementary 8-mer oligonucleotides 3'-T-5'-GCGCGCA-3' and 5'-ACGCGCGT-3'. To our knowledge, these are the first porphyrin-oligonucleotide conjugates carrying the porphyrin chromophores in the 3'-position. Chain assembly was achieved by automated solid-phase synthesis and by inexpensive straightforward 'in flask' modification of commercially available solid supported oligonucleotides. This approach allows the synthesis of modified oligonucleotides without using costly instrumentation for automated DNA synthesis. Porphyrin-containing self-complementary oligonucleotides are expected to be a valuable model for drug binding studies and determination of conformational changes in DNA sequences using circular dichroism.
Collapse
Affiliation(s)
- Milan Balaz
- Columbia University, Department of Chemistry, 3000 Broadway, New York, NY 10027, USA
| | | | | | | | | |
Collapse
|
9
|
Balaz M, Holmes AE, Benedetti M, Rodriguez PC, Berova N, Nakanishi K, Proni G. Synthesis and circular dichroism of tetraarylporphyrin-oligonucleotide conjugates. J Am Chem Soc 2005; 127:4172-3. [PMID: 15783190 DOI: 10.1021/ja043373z] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preparation and circular dichroic (CD) studies of self-complimentary 8-mer DNA sequences with a porphyrin at the 3' end are presented. Electronic interaction between the two porphyrins (the interchromophoric distance is in the range of 28-40 A), attached to both ends of the double-stranded helix, gives rise to a long-range exciton-coupled CD in the visible region (400-450 nm). The porphyrin chromophores act as sensitive probes of geometrical changes in the DNA backbone and sensitively reflect the double-strand to single-strand transition. This study demonstrates the possibility of using exciton-coupled porphyrin CDs for conformational studies of DNA.
Collapse
Affiliation(s)
- Milan Balaz
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | | | | | | | | | | | | |
Collapse
|
10
|
Crisma M, Moretto A, De Zotti M, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Turn stabilization in short peptides by C?-methylated ?-amino acids. Biopolymers 2005; 80:279-93. [PMID: 15612047 DOI: 10.1002/bip.20181] [Citation(s) in RCA: 21] [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
The crystal-state conformations of three protected tripeptides, four tetrapeptides, and one pentapeptide, heavily based on the chiral C(alpha)-methylated alpha-amino acids Iva, (alpha Me)Nva, and (Me)Val, were assessed by X-ray diffraction analyses. The eight peptide sequences are as follows: Z-(D-Iva)2-D-Val-OMe, Z-D-Iva-L-Iva-Gly-OtBu, Z-L-Pro-D-Iva-L-Iva-Gly-OtBu, Z-L-Pro-L-Iva-D-Iva-Gly-OtBu, Z-Aib-[L-(alpha Me)Nva]2-OtBu, Ac-[L-(alpha Me)Val]3-D-(alpha Me)Val-OtBu, Z-[L-(alpha Me)Val]4-OH, and Z-L-Ala-[L-(alpha Me)Nva]4-OtBu. Two independent molecules were observed in the asymmetric units of Z-D-Iva-L-Iva-Gly-OtBu and Z-Aib-[L-(alpha Me)Nva]2-OtBu, while three independent molecules were seen in Z-L-Ala-[L-(alpha Me)Nva]4-OtBu. All peptides are folded in a single or multiple beta-turn conformations. Interestingly: (i) a water bridge within the N-terminal beta-turn is seen in Z-L-Pro-L-Iva-D-Iva-Gly-OtBu (dihydrate), and (ii) the hydroxyl group of the C-terminal carboxyl functionality of Z-[L-(alpha Me)Val]4-OH generates an oxy-analogue of a beta-turn. The N-terminal beta-turn is missing in molecules A and B, but it does occur, although poorly stabilized, in molecule C, of Z-L-Ala-[L-(alpha Me)Nva]4-OtBu.
Collapse
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy.
| | | | | | | | | | | | | |
Collapse
|
11
|
Formaggio F, Peggion C, Crisma M, Kaptein B, Broxterman QB, Mazaleyrat JP, Wakselman M, Toniolo C. Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations. Chirality 2004; 16:388-97. [PMID: 15190584 DOI: 10.1002/chir.20051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.
Collapse
Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, Padova, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Toniolo C, Crisma M, Formaggio F, Peggion C, Broxterman QB, Kaptein B. Molecular spacers for physicochemical investigations based on novel helical and extended peptide structures. Biopolymers 2004; 76:162-76. [PMID: 15054896 DOI: 10.1002/bip.10575] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A proper understanding of the detailed nature and mechanism of physicochemical interactions depends heavily upon our ability to design and synthesize conformationally constrained 3D structures whose intercomponent geometry (either rigorously rigid or able to undergo destructuration, if required, but in all cases precisely tunable) would be well defined. To this end we have recently reported a few initial studies and we are currently working on the exploitation of stable, short, helical peptide spacers based on achiral and/or chiral Calpha-tetrasubstituted alpha-amino acids. These building blocks are known to force the peptides either to predominantly fold into a 3(10)-helical structure or to adopt a fully extended, planar 2.0(5)-helix. The systems under investigation involve a donor and an acceptor moiety linked to the N- and C-termini of the oligopeptide spacer main chain. By increasing the number of intervening residues the donor.acceptor separation can be easily modulated. This review highlights details of these two novel peptide secondary structures and their use as molecular spacers in physicochemical investigations.
Collapse
Affiliation(s)
- Claudio Toniolo
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy.
| | | | | | | | | | | |
Collapse
|
13
|
Proni G, Pescitelli G, Huang X, Nakanishi K, Berova N. Magnesium Tetraarylporphyrin Tweezer: a CD-Sensitive Host for Absolute Configurational Assignments of α-Chiral Carboxylic Acids. J Am Chem Soc 2003; 125:12914-27. [PMID: 14558840 DOI: 10.1021/ja036294g] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protocol to determine the absolute configuration of alpha-chiral carboxylic acids based on a modified circular dichroic (CD) exciton chirality method has been developed. The protocol relies on a host-guest complexation mechanism: the chiral substrates are derivatized to give bifunctional amide conjugates ("guests") that form complexes with a dimeric magnesium porphyrin host, Mg-T (T stands for "tweezer") that acts as a "receptor". The two porphyrins in the complex adopt a preferred helicity dictated by the substituents at the chiral center in accordance with their steric sizes (assigned on the basis of conformational energy A-values) and, consequently, with the absolute configuration of the substrates under investigation. This chiroptical method, verified with a variety of chiral substrates, has been demonstrated to be reliable and generally applicable, including natural products with complex structures. Molecular modeling, NMR, and FTIR experiments of selected host-guest complexes revealed the mode of ligation of the substrates to the magnesium porphyrin species and led to clarification of the structure of the complex. When oxygen functionalities were directly attached to the chiral center, the signs of the CD couplets were opposite to those predicted on the basis of steric size. NMR and molecular modeling experiments indicated that this apparent inconsistency was due to conformational characteristics of the guest molecules. The stereochemical analysis is shown to be a sensitive technique, not only for the determination of absolute configurations of substrates but also for elucidation of their solution conformations.
Collapse
Affiliation(s)
- Gloria Proni
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | | | | | | | |
Collapse
|
14
|
Formaggio F, Crisma M, Toniolo C, Broxterman QB, Kaptein B, Corbier C, Saviano M, Palladino P, Benedetti E. Cα-Methyl, Cα-n-Propylglycine Homo-oligomers. Macromolecules 2003. [DOI: 10.1021/ma030327v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - Catherine Corbier
- Laboratory of Crystallography, ESA 7036, Université Henry Poincaré−Nancy I, 54506 Vandoeuvre-lès-Nancy, France
| | | | | | | |
Collapse
|