1
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Keshavarzian E, Asadi Z, Poupon M, Dusek M, Rastegari B. Heterodinuclear Cu–Gd (3d-4f) complex with di-compartmental Schiff base ligand in biological activity: Synthesis, crystal structure, catecholase activity and DNA & BSA-binding studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117785] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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Zhang Q, Wang B, Zhang Y, Yang J, Deng B, Ding B, Zhong D. Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative. J Phys Chem B 2021; 125:13088-13098. [PMID: 34812635 DOI: 10.1021/acs.jpcb.1c07175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD128-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the Bb band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp5CN. We further observed a red-shift of ∼2 cm-1 and a broadening of ∼2 cm-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.
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Affiliation(s)
- Qin Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bingyao Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Yang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bodan Deng
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Robinson D, Alarfaji SS, Hirst JD. Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S 1 ← S 0 Transitions. J Phys Chem A 2021; 125:5237-5245. [PMID: 34132093 PMCID: PMC8279645 DOI: 10.1021/acs.jpca.1c01685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/05/2021] [Indexed: 11/28/2022]
Abstract
For benzene, toluene, aniline, fluorobenzene, and phenol, even sophisticated treatments of electron correlation, such as MRCI and XMS-CASPT2 calculations, show oscillator strengths typically lower than experiment. Inclusion of a simple pseudo-diabatization approach to perturb the S1 state with approximate vibronic coupling to the S2 state for each molecule results in more accurate oscillator strengths. Their absolute values agree better with experiment for all molecules except aniline. When the coupling between the S1 and S2 states is strong at the S0 geometry, the simple diabatization scheme performs less well with respect to the oscillator strengths relative to the adiabatic values. However, we expect the scheme to be useful in many cases where the coupling is weak to moderate (where the maximum component of the coupling has a magnitude less than 1.5 au). Such calculations give an insight into the effects of vibronic coupling of excited states on UV/vis spectra.
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Affiliation(s)
- David Robinson
- Department
of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United
Kingdom
| | - Saleh S. Alarfaji
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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4
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Segatta F, Rogers DM, Dyer NT, Guest EE, Li Z, Do H, Nenov A, Garavelli M, Hirst JD. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides. Molecules 2021; 26:E396. [PMID: 33451152 PMCID: PMC7828623 DOI: 10.3390/molecules26020396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Naomi T. Dyer
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China;
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
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5
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Zarei L, Asadi Z, Samolova E, Dusek M, Amirghofran Z. Pyrazolate as bridging ligand in stabilization of self-assemble Cu(II) Schiff base complexes: Synthesis, structural investigations, DNA/protein (BSA) binding and growth inhibitory effects on the MCF7, CT-26, MDA-MB-231 cell lines. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119674] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Li Z, Hirst JD. Computed optical spectra of SARS-CoV-2 proteins. Chem Phys Lett 2020; 758:137935. [PMID: 33518776 PMCID: PMC7836526 DOI: 10.1016/j.cplett.2020.137935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 02/03/2023]
Abstract
Calculated circular dichroism spectra in the far- and near-UV spectra. Calculated infra-red (IR) spectra in the amide I region. Based on experimental structures and computational models of SARS-CoV-2 proteins. Near-UV CD spectra offer greatest sensitivity to conformation.
Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models.
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Affiliation(s)
- Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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7
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Rogers DM, Jasim SB, Dyer NT, Auvray F, Réfrégiers M, Hirst JD. Electronic Circular Dichroism Spectroscopy of Proteins. Chem 2019. [DOI: 10.1016/j.chempr.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Zarei L, Asadi Z, Dusek M, Eigner V. Homodinuclear Ni (II) and Cu (II) Schiff base complexes derived from O-vanillin with a pyrazole bridge: Preparation, crystal structures, DNA and protein (BSA) binding, DNA cleavage, molecular docking and cytotoxicity study. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Jasim SB, Li Z, Guest EE, Hirst JD. DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet. J Mol Biol 2018; 430:2196-2202. [DOI: 10.1016/j.jmb.2017.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/24/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022]
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10
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Zhang HX, Zhou D, Xia QH. Study on the molecular recognition action of lamivudine by human serum albumin. J Mol Recognit 2018; 31:e2705. [DOI: 10.1002/jmr.2705] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/21/2017] [Accepted: 01/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Hua-xin Zhang
- Hubei Key Laboratory of Drug Synthesis and Optimization; Jingchu University of Technology; Jingmen Hubei People's Republic of China
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials; Hubei University; Wuhan Hubei People's Republic of China
| | - Dan Zhou
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials; Hubei University; Wuhan Hubei People's Republic of China
| | - Qing-hua Xia
- Hubei Key Laboratory of Drug Synthesis and Optimization; Jingchu University of Technology; Jingmen Hubei People's Republic of China
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials; Hubei University; Wuhan Hubei People's Republic of China
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11
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Li Z, Hirst JD. Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. Chem Sci 2017; 8:4318-4333. [PMID: 29163925 PMCID: PMC5637123 DOI: 10.1039/c7sc00586e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 11/30/2022] Open
Abstract
Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.
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Affiliation(s)
- Zhuo Li
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
| | - Jonathan D Hirst
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
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12
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Zhang HX, Zhang Q, Wang HL, Li LW. Comparison and analysis on the serum-binding characteristics of aspirin-zinc complex and aspirin. LUMINESCENCE 2017; 32:1017-1024. [DOI: 10.1002/bio.3285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/20/2016] [Accepted: 12/28/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Hua-xin Zhang
- College of Chemical and Pharmaceutical Engineering; Jingchu University of Technology; Jingmen People's Republic of China
| | - Qun Zhang
- College of Chemical and Pharmaceutical Engineering; Jingchu University of Technology; Jingmen People's Republic of China
| | - Hong-lin Wang
- College of Chemical and Pharmaceutical Engineering; Jingchu University of Technology; Jingmen People's Republic of China
| | - Li-wei Li
- College of Chemical and Pharmaceutical Engineering; Jingchu University of Technology; Jingmen People's Republic of China
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13
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Lee WQ, Affandi ISM, Feroz SR, Mohamad SB, Tayyab S. Evaluation of pendimethalin binding to human serum albumin: Insights from spectroscopic and molecular modeling approach. J Biochem Mol Toxicol 2016; 31. [DOI: 10.1002/jbt.21839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/25/2016] [Accepted: 08/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Wei Qi Lee
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science; University of Malaya; 50603 Kuala Lumpur Malaysia
| | - Ida Syazwani M. Affandi
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science; University of Malaya; 50603 Kuala Lumpur Malaysia
| | - Shevin R. Feroz
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science; University of Malaya; 50603 Kuala Lumpur Malaysia
| | - Saharuddin B. Mohamad
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science; University of Malaya; 50603 Kuala Lumpur Malaysia
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL); University of Malaya; 50603 Kuala Lumpur Malaysia
| | - Saad Tayyab
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science; University of Malaya; 50603 Kuala Lumpur Malaysia
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL); University of Malaya; 50603 Kuala Lumpur Malaysia
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14
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Zhang HX, Xiong HX, Li LW. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 161:88-94. [PMID: 26963729 DOI: 10.1016/j.saa.2016.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔH(θ)) and entropy change (ΔS(θ)) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.
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Affiliation(s)
- Hua-xin Zhang
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China
| | - Hang-xing Xiong
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China
| | - Li-wei Li
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China.
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15
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Uporov IV, Forlemu NY, Nori R, Aleksandrov T, Sango BA, Mbote YEB, Pothuganti S, Thomasson KA. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int J Mol Sci 2015; 16:21237-76. [PMID: 26370961 PMCID: PMC4613251 DOI: 10.3390/ijms160921237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/09/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023] Open
Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
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Affiliation(s)
- Igor V Uporov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia.
| | - Neville Y Forlemu
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
| | - Rahul Nori
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Tsvetan Aleksandrov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Boris A Sango
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Yvonne E Bongfen Mbote
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA.
| | - Sandeep Pothuganti
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Kathryn A Thomasson
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
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16
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Li J, Deng M, Voronine DV, Mukamel S, Jiang J. Two-dimensional near ultraviolet (2DNUV) spectroscopic probe of structural-dependent exciton dynamics in a protein. J Phys Chem B 2015; 119:1314-22. [PMID: 25544569 DOI: 10.1021/jp509314y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding the exciton dynamics in biological systems is crucial for the manipulation of their function. We present a combined quantum mechanics (QM) and molecular dynamics (MD) simulation study that demonstrates how coherent two-dimensional near-ultraviolet (2DNUV) spectra can be used to probe the exciton dynamics in a mini-protein, Trp-cage. The 2DNUV signals originate from aromatic transitions that are significantly affected by the couplings between residues, which determine exciton transport and energy relaxation. The temporal evolution of 2DNUV features captures important protein structural information, including geometric details and peptide orientations.
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Affiliation(s)
- Jun Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials, School of Chemistry and Materials Science, University of Science and Technology of China , Hefei, 230026, China
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17
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Gokarn Y, Agarwal S, Arthur K, Bepperling A, Day ES, Filoti D, Greene DG, Hayes D, Kroe-Barrett R, Laue T, Lin J, McGarry B, Razinkov V, Singh S, Taing R, Venkataramani S, Weiss W, Yang D, Zarraga IE. Biophysical Techniques for Characterizing the Higher Order Structure and Interactions of Monoclonal Antibodies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yatin Gokarn
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Sanjeev Agarwal
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Kelly Arthur
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Alexander Bepperling
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Eric S. Day
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Dana Filoti
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Daniel G. Greene
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - David Hayes
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Rachel Kroe-Barrett
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Thomas Laue
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Jasper Lin
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Brian McGarry
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Vladimir Razinkov
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Sanjaya Singh
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Rosalynn Taing
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Sathyadevi Venkataramani
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - William Weiss
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Danlin Yang
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Isidro E. Zarraga
- Institute of Chemical Technology, Mumbai, India
- Amgen Inc., Thousand Oaks, California 91320, United States
- Hexal AG, Oberhaching, Germany
- Genentech, South San Francisco, California 94080, United States
- University of New Hampshire, Durham, New Hampshire 03824, United States
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18
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Li Z, Robinson D, Hirst JD. Vibronic structure in the far-UV electronic circular dichroism spectra of proteins. Faraday Discuss 2015; 177:329-44. [DOI: 10.1039/c4fd00163j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Franck–Condon effect is considered and the vibrational structure of the πnbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and πnbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the πnbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.
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Affiliation(s)
- Zhuo Li
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
| | - David Robinson
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
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19
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Štěpánek P, Bouř P. Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions. Phys Chem Chem Phys 2014; 16:20639-49. [PMID: 25158079 DOI: 10.1039/c4cp02668c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable.
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Affiliation(s)
- Petr Štěpánek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague, Czech Republic.
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20
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21
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Chen M, Guo H, Liu Y, Zhang Q. Structural Changes of Human Serum Albumin Induced by Cadmium Acetate. J Biochem Mol Toxicol 2014; 28:281-7. [DOI: 10.1002/jbt.21564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/23/2014] [Accepted: 03/28/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Mingmao Chen
- Institute of Biomedical and Pharmaceutical Technology & College of Chemistry and Chemical Engineering; Fuzhou University; Fuzhou 350002 People's Republic of China
| | - Hao Guo
- Institute of Biomedical and Pharmaceutical Technology & College of Chemistry and Chemical Engineering; Fuzhou University; Fuzhou 350002 People's Republic of China
| | - Yan Liu
- The State Key Lab of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 People's Republic of China
| | - Qiqing Zhang
- Institute of Biomedical and Pharmaceutical Technology & College of Chemistry and Chemical Engineering; Fuzhou University; Fuzhou 350002 People's Republic of China
- Key Laboratory of Biomedical Material of Tianjin; Institute of Biomedical Engineering; Chinese Academy of Medical Science & Peking Union Medical College; Tianjin 300192 People's Republic of China
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22
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Zhang HX, Liu Y. Protein-binding properties of a designed steroidal lactam compound. Steroids 2014; 80:30-6. [PMID: 24316162 DOI: 10.1016/j.steroids.2013.11.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/19/2013] [Accepted: 11/22/2013] [Indexed: 01/18/2023]
Abstract
Introducing amide bonds into a steroid nucleus or its side chain may reduce the acute toxicity and enhance the pharmaceutical activity. In this work, a designed steroidal amide compound, named 3β-hydroxy-17-aza-d-homo-5-androsten-17-one (HAAO), was synthesized and identified. The interactions between HAAO and human serum albumin (HSA) were studied by multiple spectroscopic methods and molecular modeling procedures. It was found that HAAO locates in Sudlow's site I in subdomain IIA of HSA molecules, relying on hydrogen bonds and van der Waals power to form HAAO-HSA complexes at ground state. The number of binding sites, binding constants, enthalpy change (ΔH(θ)), Gibbs free energy change (ΔG(θ)) and entropy change (ΔS(θ)) were calculated at different temperatures based on fluorescence quenching theory and classical thermodynamic equation. The percentages content of the HSA's secondary structures in presence of HAAO were detected by circular dichroism (CD) spectra and compared with those in no presence of HAAO. In addition, the experimental results of both binding site and conformational change were further confirmed by molecular modeling investigation, in which more details of the binding were visually unfolded. The information provided by the study may be useful for designing novel chemotherapeutic drugs and be helpful both in the early stages of drug discovery and in clinical practice.
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Affiliation(s)
- Hua-Xin Zhang
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China.
| | - Y Liu
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China
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23
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Dementiev A, Swanson R, Roth R, Isetti G, Izaguirre G, Olson ST, Gettins PGW. The allosteric mechanism of activation of antithrombin as an inhibitor of factor IXa and factor Xa: heparin-independent full activation through mutations adjacent to helix D. J Biol Chem 2013; 288:33611-33619. [PMID: 24068708 DOI: 10.1074/jbc.m113.510727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allosteric conformational changes in antithrombin induced by binding a specific heparin pentasaccharide result in very large increases in the rates of inhibition of factors IXa and Xa but not of thrombin. These are accompanied by CD, fluorescence, and NMR spectroscopic changes. X-ray structures show that heparin binding results in extension of helix D in the region 131-136 with coincident, and possibly coupled, expulsion of the hinge of the reactive center loop. To examine the importance of helix D extension, we have introduced strong helix-promoting mutations in the 131-136 region of antithrombin (YRKAQK to LEEAAE). The resulting variant has endogenous fluorescence indistinguishable from WT antithrombin yet, in the absence of heparin, shows massive enhancements in rates of inhibition of factors IXa and Xa (114- and 110-fold, respectively), but not of thrombin, together with changes in near- and far-UV CD and (1)H NMR spectra. Heparin binding gives only ∼3-4-fold further rate enhancement but increases tryptophan fluorescence by ∼23% without major additional CD or NMR changes. Variants with subsets of these mutations show intermediate activation in the absence of heparin, again with basal fluorescence similar to WT and large increases upon heparin binding. These findings suggest that in WT antithrombin there are two major complementary sources of conformational activation of antithrombin, probably involving altered contacts of side chains of Tyr-131 and Ala-134 with core hydrophobic residues, whereas the reactive center loop hinge expulsion plays only a minor additional role.
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Affiliation(s)
- Alexey Dementiev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Richard Swanson
- Center for Molecular Biology of Oral Disease, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Ryan Roth
- Center for Molecular Biology of Oral Disease, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Giulia Isetti
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Gonzalo Izaguirre
- Center for Molecular Biology of Oral Disease, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Steven T Olson
- Center for Molecular Biology of Oral Disease, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Peter G W Gettins
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607.
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24
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Karabencheva-Christova TG, Carlsson U, Balali-Mood K, Black GW, Christov CZ. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study. PLoS One 2013; 8:e56874. [PMID: 23526922 PMCID: PMC3582176 DOI: 10.1371/journal.pone.0056874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 11/25/2022] Open
Abstract
Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.
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Affiliation(s)
- Tatyana G Karabencheva-Christova
- Department of Applied Sciences, School of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.
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25
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Zhang HX, Chen KS. Biophysical Studies on the Site-Selective Binding of a Synthesized Selenium–Quercetin Complex on a Protein. J SOLUTION CHEM 2012. [DOI: 10.1007/s10953-012-9844-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Zhang HX, Zhou Y, Liu E. Biophysical influence of isocarbophos on bovine serum albumin: spectroscopic probing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 92:283-288. [PMID: 22446777 DOI: 10.1016/j.saa.2012.02.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/09/2012] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
Isocarbophos (ICP) is a phosphorous pesticide with high toxicity. It has been detected in several kinds of food and therefore can enter human body. In this paper, spectroscopic approaches including three-dimensional fluorescence (3D-FL) spectroscopy, UV-visible absorption spectroscopy and circular dichroism (CD) spectroscopy were employed to explore the binding of ICP to bovine serum albumin (BSA) at simulated physiological conditions. It was found that the fluorescence quenching of BSA was caused by the formation of ICP-BSA complex at ground state and belonged to static quenching mechanism. The binding constants, the number of binding sites, enthalpy change (ΔH(θ)), Gibbs free energy change (ΔG(θ)) and entropy change (ΔS(θ)) were calculated at four different temperatures according to Scatchard model and thermodynamic equations. To identify the binding location, fluorescence probe techniques were used. The results showed that warfarin, an acknowledged site marker for BSA, could be partially replaced by ICP when ICP was added to warfarin-BSA systems, which demonstrated that ICP primarily bound on Sudlow's site I in domain IIA of BSA molecule. The distance r (3.06 nm) between donor (Trp-212) and acceptor (ICP) was obtained based on Förster's non-radiation fluorescence resonance energy transfer (FRET) theory. Furthermore, the CD spectral results indicated that the secondary structure of BSA was changed in presence of ICP. The study is helpful to evaluating the toxicology of ICP and understanding its effects on the function of protein during the blood transportation process.
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Affiliation(s)
- Hua-xin Zhang
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China.
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27
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Hudecová J, Horníček J, Buděšínský M, Šebestík J, Šafařík M, Zhang G, Keiderling TA, Bouř P. Three types of induced tryptophan optical activity compared in model dipeptides: theory and experiment. Chemphyschem 2012; 13:2748-60. [PMID: 22706803 DOI: 10.1002/cphc.201200201] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/27/2012] [Indexed: 11/08/2022]
Abstract
The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp-containing cyclic dipeptides c-(Trp-X) (where X = Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π-π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm(-1) indicates the local χ(2) angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion-corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion-DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.
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Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.
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28
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Biochemical evaluation of a synthesized isoflavone-selenium complex by molecular spectra. Mol Biol Rep 2012; 39:7457-63. [DOI: 10.1007/s11033-012-1578-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 01/30/2012] [Indexed: 11/26/2022]
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29
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30
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Zhang HX, Zhang P. Synthesis of vitamin-selenium complex and its effects on proteins and tumor cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 83:406-410. [PMID: 21925932 DOI: 10.1016/j.saa.2011.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/13/2011] [Accepted: 08/24/2011] [Indexed: 05/31/2023]
Abstract
A selenium-vitamin P complex (SEVP) was synthesized and its structure was determined by IR, LC-MS and (1)H NMR. Its biological effects on bovine serum albumin (BSA) and human colon carcinoma tumor cells were studied by molecular spectra, MTT and flow cytometry. The interaction of SEVP and BSA was discussed by fluorescence quenching method and Förster non-radiation energy transfer theory. The thermodynamic parameters ΔH(θ), ΔG(θ), ΔS(θ) at different temperatures were calculated and the results indicate the interaction is an exothermic as well as entropy-driven process. Hydrogen bond and electrostatic force played major role in the reaction. The binding geometry and conformation changes of BSA were investigated by fluorescence probe technique and circular dichroism (CD) spectra. The effects of SEVP on human colon carcinoma tumor cells HT29 were tested by MTT method and flow cytometry (FCM). The MTT results show the proliferation of HT29 tumor cells were inhibited by SEVP and the inhibition was associated with dose and time. The FCM analysis disclosed SEVP interrupted the DNA synthesis of tumor cells at S phase.
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Affiliation(s)
- Hua-xin Zhang
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei, People's Republic of China.
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31
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Zhang HX, Mei P. Synthesis of morin-zinc(II) complex and its interaction with serum albumin. Biol Trace Elem Res 2011; 143:677-87. [PMID: 21113687 DOI: 10.1007/s12011-010-8903-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 11/10/2010] [Indexed: 11/25/2022]
Abstract
A morin-zinc(II) complex (MZ) was synthesized and its interaction with bovine serum albumin (BSA) were studied by molecular spectroscopy including fluorescence emission spectra, UV-visible spectra, circular dichroism (CD) spectra, three-dimensional fluorescence spectra, and synchronous fluorescence spectra. The interaction mechanism of BSA and MZ was discussed by fluorescence quenching method and Förster non-radiation energy transfer theory. The thermodynamic parameters ΔHθ, ΔGθ, ΔSθ at different temperatures were calculated and the results indicate the interaction is an exothermic as well as entropy-driven process. Hydrogen bond forces played the most important role in the reaction. The fluorescence probe experiment showed that the binding site of MZ is in subdomain IIA of BSA and the distance between BSA and MZ is 3.17 nm at normal body temperature. The conformation changes of BSA in presence of MZ were investigated by CD spectra and three-dimensional fluorescence spectra.
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Affiliation(s)
- Hua-xin Zhang
- College of Chemical and Environmental Engineering, Yangtze University, Jingzhou, Hubei, 434023, People's Republic of China.
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32
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Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci U S A 2011; 108:12734-9. [PMID: 21768345 DOI: 10.1073/pnas.1010880108] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet-triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet-triplet energy transfer experiments on HP35.
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33
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Chemicobiological effects of herbicide MCPA-Na on plasma proteins. Mol Biol Rep 2011; 39:2745-51. [DOI: 10.1007/s11033-011-1030-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022]
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34
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Jiang J, Mukamel S. Probing amyloid fibril growth by two-dimensional near-ultraviolet spectroscopy. J Phys Chem B 2011; 115:6321-8. [PMID: 21517033 DOI: 10.1021/jp201164u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Keeping track of the aggregation kinetics of amyloid fibrils is essential for understanding their formation mechanism and eventually developing treatments for misfolded protein-related diseases. A simulation study of a series of Aβ(9-40) amyloid fibrils with different size shows that novel two-dimensional near-ultraviolet (2DNUV) spectra contain characteristic signatures of interactions between peptides. Chiral 2DNUV signals show a larger degree of exciton delocalization compared to their nonchiral counterparts. Intensities of specific peaks provide a direct measure of the number of peptides in a fibril. These signals could be used to monitor the fibril growth kinetics, one peptide at a time.
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Affiliation(s)
- Jun Jiang
- Chemistry Department, University of California, Irvine, Irvine, California 92697, USA.
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35
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Jiang J, Mukamel S. Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study. Phys Chem Chem Phys 2011; 13:2394-400. [PMID: 21132201 PMCID: PMC3141107 DOI: 10.1039/c0cp02047h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a first principles study of two dimensional electronic spectroscopy of aromatic side chain transitions in the 32-residue β-amyloid (Aβ(9-40)) fibrils in the near ultraviolet (250-300 nm). An efficient exciton Hamiltonian with electrostatic fluctuations (EHEF) algorithm is used to compute the electronic excitations in the presence of environmental fluctuations. The through-space inter- and intra-molecular interactions are calculated with high level quantum mechanics (QM) approaches, and interfaced with molecular mechanics (MM) simulations. Distinct two dimensional near ultraviolet (2DNUV) spectroscopic signatures are identified for different aromatic transitions, and the couplings between them. 2DNUV signals associated with the transition couplings are shown to be very sensitive to the change of residue-residue interactions induced by residue mutations. Our simulations suggest that 2DNUV spectra could provide a useful local probe for the structure and kinetics of fibrils.
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Affiliation(s)
- Jun Jiang
- Chemistry Department, University of California Irvine, USA
| | - Shaul Mukamel
- Chemistry Department, University of California Irvine, USA
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36
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Koehler J, Sulistijo ES, Sakakura M, Kim HJ, Ellis CD, Sanders CR. Lysophospholipid micelles sustain the stability and catalytic activity of diacylglycerol kinase in the absence of lipids. Biochemistry 2010; 49:7089-99. [PMID: 20666483 DOI: 10.1021/bi100575s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There has been a renewal of interest in interactions of membrane proteins with detergents and lipids, sparked both by recent results that illuminate the structural details of these interactions and also by the realization that some experimental membrane protein structures are distorted by detergent-protein interactions. The integral membrane enzyme diacylglycerol kinase (DAGK) has long been thought to require the presence of lipid as an obligate "cofactor" in order to be catalytically viable in micelles. Here, we report that near-optimal catalytic properties are observed for DAGK in micelles composed of lysomyristoylphosphatidylcholine (LMPC), with significant activity also being observed in micelles composed of lysomyristoylphosphatidylglycerol and tetradecylphosphocholine. All three of these detergents were also sustained high stability of the enzyme. NMR measurements revealed significant differences in DAGK-detergent interactions involving LMPC micelles versus micelles composed of dodecylphosphocholine. These results highlight the fact that some integral membrane proteins can maintain native-like properties in lipid-free detergent micelles and also suggest that C(14)-based detergents may be worthy of more widespread use in studies of membrane proteins.
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Affiliation(s)
- Julia Koehler
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8725, USA
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37
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Roy A, Bour P, Keiderling TA. TD-DFT modeling of the circular dichroism for a tryptophan zipper peptide with coupled aromatic residues. Chirality 2010; 21 Suppl 1:E163-71. [PMID: 19899143 DOI: 10.1002/chir.20792] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this work, time dependent density functional theory (TD-DFT) is used to provide a reliable basis for interpretation of the electronic spectra of coupled tryptophan (Trp) residues, particularly those in a model Trpzip beta-hairpin peptide. Pairs of isolated indoles form chiral coupled chromophores whose computed electronic ultraviolet circular dichroism (CD) is in excellent agreement with observed transition wavelengths and intensities. The calculations were compared to experimental data for pairwise coupling in mutant Trpzip peptides that are recently available. A study of variation of the basis set, geometry optimization, and the solvent environment on the spectra showed limited impact on bandshapes. An alternative simplified computational scheme, dependent on the transition dipole coupling (TDC) mechanism, is shown to give a representation of qualitative aspects of the intense CD for the (1)B bands at 228 and 213 nm. The results confirm the origin of the Trpzip diagnostic CD as primarily a dipolar interaction between Trp sidechains, and show that quantum computations of electronic CD can provide a reliable basis for interpretation of these chirally coupled aromatic spectral phenomena.
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Affiliation(s)
- Anjan Roy
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
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Karabencheva T, Christov C. Mechanisms of protein circular dichroism: insights from computational modeling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 80:85-115. [DOI: 10.1016/b978-0-12-381264-3.00003-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Structural and dynamic properties of juxta-membrane segments of caveolin-1 and caveolin-2 at the membrane interface. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:307-25. [PMID: 19847421 DOI: 10.1007/s00249-009-0548-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 09/15/2009] [Accepted: 09/24/2009] [Indexed: 12/21/2022]
Abstract
Caveolins (cav1-3) are essential membrane proteins found in caveolae. The caveolin scaffolding domain of cav-1 includes a short sequence containing a CRAC motif (V94TKYWFYR101) at its C-terminal end. To investigate the role of this motif in the caveolin-membrane interaction at the atomic level, we performed a detailed structural and dynamics characterization of a cav-1(V94-L102) nonapeptide encompassing this motif and including the first residue of cav-1 hydrophobic domain (L102), in dodecylmaltoside (DM) or dodecylphosphocholine (DPC) micelles, as membrane mimics. Cav-1(V94-L102) partitioned better in DPC and in DM/anionic lipid micelles than in DM micelles, as shown by fluorescence titration and CD. NMR data revealed that this peptide folded as an amphipathic helix located in the polar head group region of DPC micelles. The two tyrosine side-chains, flanked by arginine and lysine residues, are situated on one face of this helix, whereas the phenylalanine and tryptophan side-chains are located on the opposite face. Fluorescence studies showed significant Trp subnanosecond rotations, the presence of several rotamers, and a heterogeneous location within the water/micelle interface. NMR studies of the shorter cav-1(V94-R101) peptide and of the homologous sequence of cav-2(I79SKYVMYKF87) allowed the description of the effect of L102 and of the amino acid variations occurring in cav-2 on the structure and localization in DPC micelles. Based on the topological model of caveolins, our results suggest that the cav-1 and cav-2 nonapeptides studied form interfacial alpha-helix membrane anchors in which the K/RhhhYK/Rh motif, also found in cav-3, may play a significant role.
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Role of quantum chemical calculations in molecular biophysics with a historical perspective. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0622-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhang HX, Mei P, Yang XX. Optical, structural and thermodynamic properties of the interaction between tradimefon and serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 72:621-626. [PMID: 19119058 DOI: 10.1016/j.saa.2008.10.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 10/30/2008] [Accepted: 10/31/2008] [Indexed: 05/27/2023]
Abstract
The biological toxicity of a chloric pesticide, tradimefon to bovine serum albumin (BSA) were studied by fluorescence and absorption spectroscopy. The fluorescence quenching mechanism analysis indicates the quenching of BSA by TDF was caused by BSA-TDF complex formation and electrostatic interaction played major role in the reaction. The number of binding sites n and observed binding constant K(b) was measured by fluorescence quenching method. The thermodynamic parameters DeltaH(theta), DeltaG(theta), DeltaS(theta) at different temperatures were calculated, and the distance r between donor (BSA) and acceptor (TDF) was obtained according to Förster theory of non-radiation energy transfer. Three-dimensional fluorescence spectra, circular dichroism (CD) spectra and synchronous fluorescence spectra were used to investigate the structural change of BSA molecules with addition of TDF and the mechanism of binding reaction was analyzed at molecular level.
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Affiliation(s)
- Hua-Xin Zhang
- College of Chemical and Pharmaceutical Engineering, Jingchu University of Technology, Jingmen, Hubei 448000, People's Republic of China.
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Fluorometric probing on the binding of hematoxylin to serum albumin. Mol Biol Rep 2009; 36:2299-306. [DOI: 10.1007/s11033-009-9448-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
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Andrushchenko V, Bouř P. Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model. J Comput Chem 2008; 29:2693-703. [DOI: 10.1002/jcc.21015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Asadi A, Saboury AA, Moosavi-Movahedi A, Divsalar A, Sarbolouki MN. Interaction of bovine serum albumin with some novel PEG-containing diblock copolymers. Int J Biol Macromol 2008; 43:262-70. [DOI: 10.1016/j.ijbiomac.2008.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 05/28/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
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Synthesis of an octupolar compound and its biological effects on serum albumin. Mol Biol Rep 2008; 36:1405-11. [PMID: 18704755 DOI: 10.1007/s11033-008-9329-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
A special rigid planar structural octupolar molecule titled 2,4,6-tris(p-methylstyryl)-s-triazine (TMT) was synthesized and its interaction with bovine serum albumin (BSA) were studied by molecular spectroscopy. The quenching mechanism of fluorescence of BSA by TMT was discussed. The thermodynamic parameters DeltaH(theta), DeltaG(theta), DeltaS(theta) at different temperatures were calculated and the results indicate hydrogen bond forces played major role in the reaction and the reaction was mainly enthalpy-driven. The distance r between donor (BSA) and acceptor (TMT) was obtained according to Förster theory of non-radiation energy transfer. Circular dichroism (CD) spectra, synchronous and three-dimensional fluorescence spectra were used to investigate the structural change of BSA molecules with addition of TMT, the result indicates that the alpha-helical structures of BSA molecules reduced in the presence of TMT. Sketch map of the interaction process was analyzed at molecular level.
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Christov CZ, Karabencheva TG, Lodola A. Relationship between chiroptical properties, structural changes and interactions in enzymes: A computational study on β-lactamases from class A. Comput Biol Chem 2008; 32:167-75. [DOI: 10.1016/j.compbiolchem.2008.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/06/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
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Christov C, Karabencheva T, Lodola A. Aromatic interactions and rotational strengths within protein environment: An electronic structural study on β-lactamases from class A. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.012] [Citation(s) in RCA: 6] [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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Bulheller BM, Miles AJ, Wallace BA, Hirst JD. Charge-Transfer Transitions in the Vacuum-Ultraviolet of Protein Circular Dichroism Spectra. J Phys Chem B 2008; 112:1866-74. [DOI: 10.1021/jp077462k] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin M. Bulheller
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom, and Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
| | - Andrew J. Miles
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom, and Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
| | - B. A. Wallace
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom, and Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom, and Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
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Ran D, Wu X, Zheng J, Yang J, Zhou H, Zhang M, Tang Y. Study on the Interaction between Florasulam and Bovine Serum Albumin. J Fluoresc 2007; 17:721-6. [PMID: 17703351 DOI: 10.1007/s10895-007-0226-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 07/17/2007] [Indexed: 11/24/2022]
Abstract
In this paper, the interaction between florasulam (FU, 2',6',8-trifluoro-5-methoxy [Kragh-Hansen U, Molecular aspects of ligand binding to serum albumin. Pharmacol Rev 33(1):17-53 1981; Carter DC and Ho JX, Structure of serum albumin. Adv Protein Chem 45:153-203 1994; He XM, and Carter DC, Atomic structure and chemistry of human serum albumin. Nature 358(6383):209-215 1992] triazolo [1,5-c]pyrimidine-2-sulfonanilide) and bovine serum albumin (BSA) was investigated by fluorescence, ultraviolet absorption (UV) and Far-UV circular dichroism (CD) spectrometries. A strong fluorescence quenching was observed and the quenching mechanism was considered as static quenching. The binding constant of FU with BSA at 299 and 309 K were obtained as 1.5 x 10(4) and 7.1 x 10(3) l mol(-1), respectively. There was one binding site between FU and BSA. The thermodynamic parameters enthalpy change (DeltaH) and entropy change (DeltaS) were calculated as -57.89 kJ mol(-1) and -113.6 J mol(-1) K(-1), respectively, which indicated that the acting force between FU and BSA was mainly hydrogen bond and Van der Waals force. According to the Förster non-radiation energy transfer theory, the average binding distance between donor (BSA) and acceptor (FU) was obtained (r = 1.59 nm). The investigations of the UV/Vis and CD spectra of the system showed that the conformation of BSA was changed in presence of FU.
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Affiliation(s)
- Dehuan Ran
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, People's Republic of China
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