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Das D, Yadav P, Mitra S, Ainavarapu SRK. Metal-binding and circular permutation-dependent thermodynamic and kinetic stability of azurin. Proteins 2023; 91:634-648. [PMID: 36511110 DOI: 10.1002/prot.26454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three-dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β-barrel, β-sandwich, β-α-β, and all α-Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin-in both metal-free and metal-bound (holo) forms. As observed earlier in other proteins, apo-forms of wild-type (WT) and cpN42 fold with similar rates. In contrast, zinc-binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc-binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc-binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Priya Yadav
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Soumyajit Mitra
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
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2
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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3
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Sasidharanpillai S, Loppnow GR. Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy. J Phys Chem B 2019; 123:3898-3906. [PMID: 30973725 DOI: 10.1021/acs.jpcb.9b01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.
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Affiliation(s)
| | - Glen R Loppnow
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G 2G2 , Canada
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4
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Billinghurst BE, Oladepo SA, Loppnow GR. Initial excited-state structural dynamics of thymine derivatives. J Phys Chem B 2012; 116:10496-503. [PMID: 22697627 DOI: 10.1021/jp301952v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry. The UV resonance Raman spectrum of thymidine and thymidine 5'-monophosphate are similar to that of thymine, suggesting that large masses at N(1) effectively isolate the vibrations of the nucleobase. However, the UV resonance Raman spectrum of N(1)-methylthymine is significantly different, suggesting that the methyl group couples into the thymine ring vibrations. The resulting resonance Raman intensities and absorption spectra are self-consistently simulated with a time-dependent expression to quantitatively extract the initial excited-state slopes, homogeneous and inhomogeneous linewidths, and electronic parameters. These results are discussed in the context of the known photochemistry of thymine and its derivatives.
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Affiliation(s)
- Brant E Billinghurst
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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5
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El-Yazbi AF, Palech A, Loppnow GR. Initial Excited-State Structural Dynamics of 2′-Deoxyguanosine Determined via UV Resonance Raman Spectroscopy. J Phys Chem A 2011; 115:10445-51. [DOI: 10.1021/jp205166j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alexandra Palech
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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6
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Oladepo SA, Loppnow GR. Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy. J Phys Chem B 2011; 115:6149-56. [DOI: 10.1021/jp1095294] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sulayman A. Oladepo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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7
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Blanco-Rodríguez AM, Busby M, Ronayne K, Towrie M, Grădinaru C, Sudhamsu J, Sýkora J, Hof M, Záliš S, Di Bilio AJ, Crane BR, Gray HB, Vlček A. Relaxation Dynamics of Pseudomonas aeruginosa ReI(CO)3(α-diimine)(HisX)+ (X = 83, 107, 109, 124, 126)CuII Azurins. J Am Chem Soc 2009; 131:11788-800. [DOI: 10.1021/ja902744s] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana María Blanco-Rodríguez
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Michael Busby
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Kate Ronayne
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Michael Towrie
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Cristian Grădinaru
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Jawahar Sudhamsu
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Jan Sýkora
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Martin Hof
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Stanislav Záliš
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Angel J. Di Bilio
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Brian R. Crane
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Harry B. Gray
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
| | - Antonín Vlček
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom, Central Laser Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Beckman Institute, California Institute
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8
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Bose S, Adhikary R, Mukherjee P, Song X, Petrich JW. Considerations for the Construction of the Solvation Correlation Function and Implications for the Interpretation of Dielectric Relaxation in Proteins. J Phys Chem B 2009; 113:11061-8. [DOI: 10.1021/jp9004345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sayantan Bose
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | | | - Prasun Mukherjee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Xueyu Song
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Jacob W. Petrich
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
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9
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10
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Halder M, Mukherjee P, Bose S, Hargrove MS, Song X, Petrich JW. Solvation dynamics in protein environments: Comparison of fluorescence upconversion measurements of coumarin 153 in monomeric hemeproteins with molecular dynamics simulations. J Chem Phys 2007; 127:055101. [PMID: 17688362 DOI: 10.1063/1.2753495] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complexes of the fluorescence probe coumarin 153 with apomyoglobin and apoleghemoglobin are used as model systems to study solvation dynamics in proteins. Time-resolved Stokes shift experiments are compared with molecular dynamics simulations, and very good agreement is obtained. The solvation of the coumarin probe is very rapid with approximately 60% occurring within 300 fs and is attributed to interactions with water (or possibly to the protein itself). Differences in the solvation relaxation (or correlation) function C(t) for the two proteins are attributed to differences in their hemepockets.
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Affiliation(s)
- Mintu Halder
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
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11
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Ng S, Yarasi S, Brost P, Loppnow GR. Initial Excited-State Structural Dynamics of Thymine Are Coincident with the Expected Photochemical Dynamics. J Phys Chem A 2007; 111:5130-5. [PMID: 17530833 DOI: 10.1021/jp071443t] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To explore the excited-state structural dynamics of thymine, a DNA nucleobase, we measured the resonance Raman spectra of thymine in aqueous solution at wavelengths throughout the lowest-energy absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yielded the excited-state structural dynamics. The photochemically relevant C=C stretching and C-H deformation vibrational modes were found to exhibit maximum resonance Raman intensity and structural change upon photoexcitation for thymine, suggesting that the initial dynamics of thymine lie along the photochemical reaction coordinate.
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Affiliation(s)
- Susan Ng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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12
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Chowdhury PK, Halder M, Sanders L, Arnold RA, Liu Y, Armstrong DW, Kundu S, Hargrove MS, Song X, Petrich JW. The Complex of Apomyoglobin with the Fluorescent Dye Coumarin 153¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2004.tb00032.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Shoute LCT, Helburn R, Kelley AM. Solvent Effects on the Resonance Raman and Hyper-Raman Spectra and First Hyperpolarizability of N,N-Dipropyl-p-nitroaniline. J Phys Chem A 2007; 111:1251-8. [PMID: 17256826 DOI: 10.1021/jp066599s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Linear absorption spectra, resonance Raman spectra and excitation profiles, and two-photon-resonant hyper-Rayleigh and hyper-Raman scattering hyperpolarizability profiles are reported for the push-pull chromophore N,N-dipropyl-p-nitroaniline in seven solvents spanning a wide range of polarities. The absorption spectral maximum red shifts by about 2700 cm(-1), and the symmetric -NO2 stretch shifts to lower frequencies by about 11 cm(-1) from hexane to acetonitrile, indicative of significant solvent effects on both the ground and excited electronic states. The intensity patterns in the resonance Raman and hyper-Raman spectra are similar and show only a small solvent dependence except in acetonitrile, where both the Raman and hyper-Raman intensities are considerably reduced. Quantitative modeling of all four spectroscopic observables in all seven solvents reveals that the origin of this effect is an increased solvent-induced homogeneous broadening in acetonitrile. The linear absorption oscillator strength is nearly solvent-independent, and the peak resonant hyperpolarizability, beta(-2omega;omega,omega), varies by only about 15% across the wide range of solvents examined. These results suggest that the resonant two-photon absorption cross sections in this chromophore should exhibit only a weak solvent dependence.
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Affiliation(s)
- Lian C T Shoute
- School of Natural Sciences, University of California, Merced, P.O. Box 2039, Merced, California 95344, USA
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14
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Mukherjee P, Haider M, Hargrove MS, Petrich JW. Characterization of the Interactions of Fluorescent Probes with Proteins: Coumarin 153 and 1,8-ANS in Complex with Holo- and Apomyoglobin. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09815.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Billinghurst BE, Yeung R, Loppnow GR. Excited-State Structural Dynamics of 5-Fluorouracil. J Phys Chem A 2006; 110:6185-91. [PMID: 16686451 DOI: 10.1021/jp0609333] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Fluorouracil is an analogue of thymine and uracil, nucleobases found in DNA and RNA, respectively. The photochemistry of thymine is significant; UV-induced photoproducts of thymine in DNA lead to skin cancer and other diseases. In previous work, we have suggested that the differences in the excited-state structural dynamics of thymine and uracil arise from the methyl group in thymine acting as a mass barrier, localizing the vibrations at the photochemical active site. To further test this hypothesis, we have measured the resonance Raman spectra of 5-fluorouracil at wavelengths throughout its 267 nm absorption band. The spectra of 5-fluorouracil and thymine are very similar. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism suggests that, at most, 81% of the reorganization energy upon excitation is directed along photochemically relevant modes. This compares well with what was found for thymine, supporting the mass barrier hypothesis.
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Affiliation(s)
- Brant E Billinghurst
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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16
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Billinghurst BE, Loppnow GR. Excited-State Structural Dynamics of Cytosine from Resonance Raman Spectroscopy. J Phys Chem A 2006; 110:2353-9. [PMID: 16480294 DOI: 10.1021/jp0561571] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytosine, a nucleobase found in both DNA and RNA, is known to form photoproducts upon UV irradiation, damaging the nucleic acids and leading to cancer and other diseases. To determine the molecular mechanism by which these photoproducts occur, we have measured the resonance Raman spectra of cytosine at wavelengths throughout its 267 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yields both the excited-state structural changes and electronic parameters. From this analysis, we have been able to determine that, at most, 31% of the reorganization energy upon excitation is directed along photochemically relevant modes.
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Affiliation(s)
- Brant E Billinghurst
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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17
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Flemming Hansen D, Gorelsky SI, Sarangi R, Hodgson KO, Hedman B, Christensen HEM, Solomon EI, Led JJ. Reinvestigation of the method used to map the electronic structure of blue copper proteins by NMR relaxation. J Biol Inorg Chem 2006; 11:277-85. [PMID: 16432723 DOI: 10.1007/s00775-005-0070-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 11/29/2005] [Indexed: 10/25/2022]
Abstract
A previous method for mapping the electron spin distribution in blue copper proteins by paramagnetic nuclear magnetic resonance (NMR) relaxation (Hansen DF, Led JJ, 2004, J Am Chem Soc 126:1247-1253) suggested that the blue copper site of plastocyanin from Anabaena variabilis (A.v.) is less covalent than those found for other plastocyanins by other experimental methods, such as X-ray absorption spectroscopy. Here, a detailed spectroscopic study revealed that the electronic structure of A.v. plastocyanin is similar to those of other plastocyanins. Therefore, the NMR approach was reinvestigated using a more accurate geometric structure as the basis for the mapping, in contrast to the previous approach, as well as a more complete spin distribution model including Gaussian-type natural atomic orbitals instead of Slater-type hydrogen-like atomic orbitals. The refinement results in a good agreement between the electron spin density derived from paramagnetic NMR and the electronic structure description obtained by the other experimental methods. The refined approach was evaluated against density functional theory (DFT) calculations on a model complex of the metal site of plastocyanin in the crystal phase. In general, the agreement between the experimental paramagnetic relaxation rates and the corresponding rates obtained by the DFT calculations is good. Small deviations are attributed to minor differences between the solution structure and the crystal structure outside the first coordination sphere. Overall, the refined approach provides a complementary experimental method for determining the electronic structure of paramagnetic metalloproteins, provided that an accurate geometric structure is available.
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Affiliation(s)
- D Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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18
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Mukherjee P, Halder M, Hargrove MS, Petrich JW. Characterization of the Interactions of Fluorescent Probes with Proteins: Coumarin 153 and 1,8-ANS in Complex with Holo- and Apomyoglobin. Photochem Photobiol 2006; 82:1586-90. [PMID: 16961435 DOI: 10.1562/2006-07-06-ra-962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In order to provide a thorough characterization of a system with which to study the dielectric response of a protein, a well-defined system complex of a fluorescent probe and protein is required. We have argued that such a system is provided by coumarin 153 and apomyoglobin (Photochem. Photobiol. 79, 440-446 [2004]). In order to demonstrate further that coumarin 153 exhibits negligible nonspecific binding to the surface of apomyoglobin, we study its interactions with both the apo and holo proteins. We further make a similar comparison with 8-anilino-l-naphthalenesulfonic acid, for which an NMR structure with apomyoglobin has been obtained. Our results confirm the appropriateness of the system of coumarin 153 and apomyoglobin for the investigation of solvation by the protein matrix.
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Affiliation(s)
- Prasun Mukherjee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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19
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Chowdhury PK, Halder M, Sanders L, Arnold RA, Liu Y, Armstrong DW, Kundu S, Hargrove MS, Song X, Petrich JW. The complex of apomyoglobin with the fluorescent dye coumarin 153. Photochem Photobiol 2004; 79:440-6. [PMID: 15191053 DOI: 10.1562/ra-020r.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Understanding a protein's dielectric response requires both a theoretical model and a well-defined experimental system. The former has already been proposed by Song (J. Chem. Phys. 116, 9359 [2002]). We suggest that the latter is provided by the complex of coumarin 153 (C153) with apomyoglobin (ApoMb). C153 has been exhaustively studied and has proven to be an excellent probe of the solvation dynamics of polar solvents. Myoglobin is one of the most thoroughly studied proteins. Myoglobins from a wide range of species have been subject to X-ray structural analysis and site-directed mutagenesis. Here, we demonstrate the existence of a robust C153-apomyglobin system by means of molecular dynamics simulations, equilibrium binding studies using a Job's plot and capillary electrophoresis, circular dichroism and time-resolved fluorescence. The reorganization energy of C153 bound to ApoMb is compared with that of C153 in bulk solvent using the method of Jordanides et al. (J. Phys. Chem. B 103, 7995 [1999]).
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Affiliation(s)
- P K Chowdhury
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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Beyere L, Arboleda P, Monga V, Loppnow GR. The dependence of thymine and thymidine Raman spectra on solvent. CAN J CHEM 2004. [DOI: 10.1139/v04-052] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent work has focused on developing Raman spectroscopy as a noninvasive probe of DNA interactions with solvents, intercalants, proteins, and other ligands. Here, we report the Raman spectra of thymine in eight solvents and thymidine in nine solvents obtained with visible excitation. Raman spectra under acidic, neutral, and basic conditions were also obtained of both thymine and thymidine. Changes in both the frequencies and intensities of several of the vibrational bands in the 8001800 cm1 region are observed. No evidence of deprotonation in the different solvents is observed for either thymine or thymidine. Correlations of the observed frequency shifts of specific vibrational modes with characteristic properties of the solvent for both thymine and thymidine show a significant correlation with acceptor and donor numbers, measures of the hydrogen-bonding ability of the solvent, in both thymine and thymidine. These results are interpreted in terms of hydrogen-bonding interactions between the N-H protons of the thymine base and lone pairs of electrons on the solvent molecules and between the solvent hydrogens and lone pairs on C=O sites. The solvent-dependent intensity in vibrational bands of thymine between 1500 and 1800 cm1 indicates a strong interaction between thymine and solvent at the C=O and N-H sites that leads to separation of the C=O stretches from the C=C stretch. The intensity variations with solvent were much smaller for thymidine than for thymine, perhaps as a result of replacing the N1 proton by the sugar. These results suggest that Raman spectroscopy is uniquely sensitive to specific interactions of thymine and thymidine with their environment.Key words: Raman spectroscopy, thymine, thymidine, solvent effects, hydrogen bonding.
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Solomon EI, Szilagyi RK, DeBeer George S, Basumallick L. Electronic Structures of Metal Sites in Proteins and Models: Contributions to Function in Blue Copper Proteins. Chem Rev 2004; 104:419-58. [PMID: 14871131 DOI: 10.1021/cr0206317] [Citation(s) in RCA: 669] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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22
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Fraga E, Loppnow GR. The Role of Specific Amino Acid Residues in The Vibrational Properties of Plastocyanin. J Phys Chem B 2002. [DOI: 10.1021/jp014547r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Fraga
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - G. R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Moran AM, Bartholomew GP, Bazan GC, Kelley AM. Effects of a Paracyclophane Linker on the Charge-Transfer Transition of 4-(Dimethylamino)-4‘-nitrostilbene. J Phys Chem A 2002. [DOI: 10.1021/jp025504t] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Moran
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506-3701, and Department of Chemistry and Materials, University of California, Santa Barbara, California 93106
| | - Glenn P. Bartholomew
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506-3701, and Department of Chemistry and Materials, University of California, Santa Barbara, California 93106
| | - Guillermo C. Bazan
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506-3701, and Department of Chemistry and Materials, University of California, Santa Barbara, California 93106
| | - Anne Myers Kelley
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506-3701, and Department of Chemistry and Materials, University of California, Santa Barbara, California 93106
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Webb MA, Loppnow GR. Evidence for Anisotropic Coupling between the Protein Environment and the Copper Site in Azurin from Resonance Raman Spectroscopy. J Phys Chem B 2002. [DOI: 10.1021/jp013665b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Adam Webb
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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25
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Changenet-Barret P, Choma CT, Gooding EF, DeGrado WF, Hochstrasser RM. Ultrafast Dielectric Response of Proteins from Dynamics Stokes Shifting of Coumarin in Calmodulin. J Phys Chem B 2000. [DOI: 10.1021/jp001634v] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jordanides XJ, Lang MJ, Song X, Fleming GR. Solvation Dynamics in Protein Environments Studied by Photon Echo Spectroscopy. J Phys Chem B 1999. [DOI: 10.1021/jp9910993] [Citation(s) in RCA: 282] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xanthipe J. Jordanides
- Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Matthew J. Lang
- Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Xueyu Song
- Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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Webb MA, Loppnow GR. A Structural Basis for Long-Range Coupling in Azurins from Resonance Raman Spectroscopy. J Phys Chem A 1999. [DOI: 10.1021/jp991434n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Adam Webb
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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