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Kumaran R, Gayathri S, Augustine Arul Prasad T, Dhenadhayalan N, Keerthiga R, Sureka S, Jeevitha K, Karthick P. Fluorescence and quantum mechanical approach on the interaction of amides and their role on the stability and coexistence of the rotamer conformations of L-tryptophan in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 243:118791. [PMID: 32810781 DOI: 10.1016/j.saa.2020.118791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Photophysical investigation on the fluorescence decay characteristics of L-tryptophan and a derivative N-acetyl-L-tryptophanamide (NATA) with alkyl amides were carried out in water. L-tryptophan exists in the zwitterionic form and exhibits a biexponential lifetime which is correlated to the existence of rotamer structures. Addition of formamide (F) and dimethylformamide (DMF) results in a decrease in the fluorescence lifetime and its proportion of the most stable structure of L-tryptophan wherein acetamide (ACM) results in an increase of the same. Interestingly, all the amides result in the formation of the lifetime of the rotamer whose lifetime doesn't exist initially and the lifetime and its distribution increases irrespective of the nature of amide. The interaction between L-tryptophan and amide is attributed to hydrogen-bonding such that these interactions influence the relative proportion of the existence of individual rotamers in the presence of amides.Strikingly, in the case of NATA that does not exhibit rotamer structures; the fluorescence lifetime is quenched in the presence of F, whereas ACM and DMF result in a larger fold of enhancement resulting in two different lifetimes. The variation in the fluorescence lifetime and amplitude of the various conformers of L-tryptophan and of NATA is completely governed by the concentration of the amides in solution such that the microenvironment surrounding the fluorophores are completely reorganised. The hydrogen-bonding functional groups in amides that are responsible for the coexistence of rotamers are elucidated and well supported by quantum mechanical (QM) studies. Time-correlated single-photon counting(TCSPC) technique is used as a probe as well as marker in establishing the variation in the lifetime properties of L-tryptophan and NATA with non-fluorescent hydrogen-bonding solutes in water which promotes this as fascinating field of research in the context of fluorescence properties of a complicated amino acid-like tryptophan.
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Affiliation(s)
- Rajendran Kumaran
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India.
| | - Somasundaram Gayathri
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Thomas Augustine Arul Prasad
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | | | - Ravichandran Keerthiga
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Suresh Sureka
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Kumar Jeevitha
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Pargunan Karthick
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R.Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
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Eisenberg AS, Nathan M, Juszczak LJ. Excited state electron distribution and role of the terminal amine in acidic and basic tryptophan dipeptide fluorescence. J Mol Struct 2016; 1118:56-67. [DOI: 10.1016/j.molstruc.2016.03.098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rolinski OJ, Vyshemirsky V. Fluorescence kinetics of tryptophan in a heterogeneous environment. Methods Appl Fluoresc 2014; 2:045002. [DOI: 10.1088/2050-6120/2/4/045002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Horn AHC. A consistent force field parameter set for zwitterionic amino acid residues. J Mol Model 2014; 20:2478. [PMID: 25338816 DOI: 10.1007/s00894-014-2478-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 09/21/2014] [Indexed: 12/20/2022]
Abstract
Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
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Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstr. 17, 91054, Erlangen, Germany,
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Méndez-Hurtado J, Isabel Menéndez M, López R, Ruiz-López MF. An ab initio analysis of the structure of l-tryptophan tautomers in microhydrated environments, in water and in hydrophobic solvents. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Boeckx B, Maes G. The conformational behavior and H-bond structure of asparagine: A theoretical and experimental matrix-isolation FT-IR study. Biophys Chem 2012; 165-166:62-73. [DOI: 10.1016/j.bpc.2012.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 03/11/2012] [Accepted: 03/12/2012] [Indexed: 11/16/2022]
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Boeckx B, Nelissen W, Maes G. Potential Energy Surface and Matrix Isolation FT-IR Study of Isoleucine. J Phys Chem A 2012; 116:3247-58. [DOI: 10.1021/jp212240p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Wouter Nelissen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
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Lorenzo AC, Bisch PM. Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules. J Mol Graph Model 2008; 24:59-71. [PMID: 16002307 DOI: 10.1016/j.jmgm.2005.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 05/11/2005] [Accepted: 05/11/2005] [Indexed: 11/23/2022]
Abstract
The aim of this report is two-fold: First, to show the applicability of the Steered Molecular Dynamics (SMD) methodology for analyzing non-specific interactions governing the membrane affinity process of small biological molecules. Second, to point out a correlation between the system response and certain combinations of the SMD parameters (spring-elastic-constant and pulling-group). For these purposes, a simplified membrane model was used, modeled as a non-polar region limited by two polar aqueous media in a continuous dielectric representation. Polarization-induced effects at both interfaces were taken into account by the "electrostatic images" method. To perform SMD simulations a harmonic external force, representing a spring acting on a selected atom, forces the molecule to "break" its interaction with the surrounding environment by extracting it out of the membrane. With this approach, small molecules and peptides, with known affinity for the membrane environment, were studied: the zwitterionic tryptophan residue and a pentapeptide AcWLKLL. The SMD parameters, spring-elastic-constant and pulling-group, were varied and combined in order to analyze the systems responses in each case. It was observed that, the spring stiffness was crucial to reveal specific events that occur during the molecule behavior; hence, it was directly responsible for the sensitivity of this methodology. The pulling-group selected highly influenced on the reaction pathway, a fact that it was not observed with other parameters; consequently, force profiles are like the "fingerprints" of these induced pathways. The potential profile for the tryptophan was recovered from the SMD simulations being in good agreement with that estimated by an approximation method. With this rather simple model approach, SMD methodology has proven to be suitable for revealing the main interactions that govern the membrane affinity processes of small molecules and peptides.
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Affiliation(s)
- Alicia C Lorenzo
- Laboratório de Dinâmica Molecular, Programa de Computação Científica, PROCC, Fundação Oswaldo Cruz, FIOCRUZ, Av. Brasil, 4365 Manguinhos, 21045-900 Rio de Janeiro, Brazil.
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Guzow K, Rzeska A, Mrozek J, Karolczak J, Majewski R, Szabelski M, Ossowski T, Wiczk W. Photophysical Properties of Tyrosine and Its Simple Derivatives in Organic Solvents Studied by Time-resolved Fluorescence Spectroscopy and Global Analysis¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00246.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bombasaro J, Rodríguez A, Enriz R. Comprehensive conformational analysis of N-acetyl-l-tryptophane-N-methylamide. An ab initio and DFT study. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.11.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ahn DS, Kang AR, Lee S, Kim B, Kyu Kim S, Neuhauser D. On the stability of glycine-water clusters with excess electron: Implications for photoelectron spectroscopy. J Chem Phys 2005; 122:84310. [PMID: 15836042 DOI: 10.1063/1.1850893] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Calculations are presented for the glycine-(H(2)O)(n) (-) (n=0-2) anionic clusters with excess electron, with the glycine core in the canonical or zwitterion form. A variety of conformers are predicted, and their relative energy is examined to estimate thermodynamic stability. The dynamic (proton transfer) pathways between the anionic clusters with the canonical and the zwitterion glycine core are examined. Small barrier heights for isomerization from the zwitterion glycine-(H(2)O)(2) (-) anion to those with canonical glycine core suggest that the former conformers may be kinetically unstable and unfavorable for detection of neutral glycine zwitterion-(H(2)O)(n) (n=1,2) clusters by photodetachment, in accordance with the photoelectron spectroscopic experiments by Bowen and co-workers [Xu et al., J. Chem. Phys. 119, 10696 (2003)]. The calculated stability of the glycine-(H(2)O)(n) (-) anion clusters with canonical glycine core relative to those with zwitterion core indicates that the observation of the anionic conformers with the canonical glycine core would be much more feasible, as revealed by Johnson and co-workers [Diken et al. J. Chem. Phys. 120, 9902 (2004)].
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Affiliation(s)
- Doo-Sik Ahn
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
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Abstract
The peptide bond quenches tryptophan fluorescence by excited-state electron transfer, which probably accounts for most of the variation in fluorescence intensity of peptides and proteins. A series of seven peptides was designed with a single tryptophan, identical amino acid composition, and peptide bond as the only known quenching group. The solution structure and side-chain chi(1) rotamer populations of the peptides were determined by one-dimensional and two-dimensional (1)H-NMR. All peptides have a single backbone conformation. The -, psi-angles and chi(1) rotamer populations of tryptophan vary with position in the sequence. The peptides have fluorescence emission maxima of 350-355 nm, quantum yields of 0.04-0.24, and triple exponential fluorescence decays with lifetimes of 4.4-6.6, 1.4-3.2, and 0.2-1.0 ns at 5 degrees C. Lifetimes were correlated with ground-state conformers in six peptides by assigning the major lifetime component to the major NMR-determined chi(1) rotamer. In five peptides the chi(1) = -60 degrees rotamer of tryptophan has lifetimes of 2.7-5.5 ns, depending on local backbone conformation. In one peptide the chi(1) = 180 degrees rotamer has a 0.5-ns lifetime. This series of small peptides vividly demonstrates the dominant role of peptide bond quenching in tryptophan fluorescence.
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Affiliation(s)
- Chia-Pin Pan
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
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Guzow K, Rzeska A, Mrozek J, Karolczak J, Majewski R, Szabelski M, Ossowski T, Wiczk W. Photophysical Properties of Tyrosine and Its Simple Derivatives in Organic Solvents Studied by Time-resolved Fluorescence Spectroscopy and Global Analysis¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-03-02-ra-095.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bingham NC, Smith NEC, Cross TA, Busath DD. Molecular dynamics simulations of Trp side-chain conformational flexibility in the gramicidin A channel. Biopolymers 2004; 71:593-600. [PMID: 14635099 DOI: 10.1002/bip.10546] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gramicidin A (gA) is prototypical peptide antibiotic and a model ion channel former. Configured in the solid-state NMR beta(6.5)-helix channel conformation, gA was subjected to 1-ns molecular dynamics (MD) gas phase simulations using the all-atom charmm22 force field to ascertain the conformational stability of the Trp side chains as governed by backbone and neighboring side-chain contacts. Three microcanonical trajectories were computed using different initial atomic velocities for each of twenty different initial structures. For each set, one of the four Trp side chains in each monomer was initially positioned in one of the five non-native conformations (A. E. Dorigo et al., Biophysical Journal, 1999, Vol. 76, 1897-1908), the other Trps being positioned in the native state, o1. In three additional control simulations, all Trps were initiated in the native conformation. After equilibration, constraints were removed and subsequent conformational changes of the initially constrained Trp were measured. The chi(1) was more flexible than chi(2.1). The energetically optimal orientation, o1 (Dorigo et al., 1999), was the most stable in all four Trp positions (9, 11, 13, 15) and remained unchanged for the entire 1 ns simulation in 19 of 24 trials. Changes in chi(1) from each of the 5 suboptimal states occur readily. Two of the non-native conformations reverted readily to o1, whereas the other three converted to an intermediate state, i2. There were frequent interconversions between i2 and o1. We speculate that experimentally observed Trp stability is caused by interactions with the lipid-water interface, and that stabilization of one of the suboptimal conformations in gA, such as i2, by lipid headgroups could produce a secondary, metastable conformational state. This could explain recent experimental studies of differences in the channel conductance dispersity between gA and a Trp-to-Phe gA analog, gramicidin M (gM, J. C. Markham et al., Biochimica et Biophysica Acta, 2001, Vol. 1513, 185-192).
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Affiliation(s)
- Nathan C Bingham
- Department of Physiology and Developmental Biology and Center for Neuroscience, Brigham Young University, Provo, UT 84602, USA.
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Lioe H, O'Hair RAJ, Reid GE. Gas-phase reactions of protonated tryptophan. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:65-76. [PMID: 14698557 DOI: 10.1016/j.jasms.2003.09.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen-deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H - NH(3)](+) ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen-deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH(3) loss.
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Affiliation(s)
- Hadi Lioe
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
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Ahn DS, Park SW, Jeon IS, Lee MK, Kim NH, Han YH, Lee S. Effects of Microsolvation on the Structures and Reactions of Neutral and Zwitterion Alanine: Computational Study. J Phys Chem B 2003. [DOI: 10.1021/jp031041v] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Doo-Sik Ahn
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - Sung-Woo Park
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - In-Sun Jeon
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - Min-Kyung Lee
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - Nam-Hee Kim
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - Young-Hwa Han
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
| | - Sungyul Lee
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
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Exploratory conformational analysis of N-acetyl-L-Tryptophan-N-methylamide. An ab initio study. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00261-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Larsen OFA, van Stokkum IHM, Pandit A, van Grondelle R, van Amerongen H. Ultrafast Polarized Fluorescence Measurements on Tryptophan and a Tryptophan-Containing Peptide. J Phys Chem B 2003. [DOI: 10.1021/jp021756i] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olaf F. A. Larsen
- Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Department of Structural Biology, Faculty of Earth and Lifesciences, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Ivo H. M. van Stokkum
- Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Department of Structural Biology, Faculty of Earth and Lifesciences, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Anjali Pandit
- Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Department of Structural Biology, Faculty of Earth and Lifesciences, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Rienk van Grondelle
- Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Department of Structural Biology, Faculty of Earth and Lifesciences, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Herbert van Amerongen
- Division of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Department of Structural Biology, Faculty of Earth and Lifesciences, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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Park SW, Ahn DS, Lee S. Dynamic paths between neutral alanine–water and zwitterionic alanine–water clusters: single, double and triple proton transfer. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00221-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Influence of a substituent on amide nitrogen atom on fluorescence efficiency quenching of Tyr(Me) by amide group. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00521-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Malicka J, Groth M, Karolczak J, Czaplewski C, Liwo A, Wiczk W. Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues. Biopolymers 2001; 58:447-57. [PMID: 11180057 DOI: 10.1002/1097-0282(20010405)58:4<447::aid-bip1020>3.0.co;2-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fluorescence decay of tryptophan is a sensitive indicator of its local environment within a peptide or protein. In this study we carried out fluorescence measurements of the tryptophan residue of cyclic enkephalin analogues of a general formula X-c[D-Dab(2)-Gly(3)-Trp(4)-Y(5)] where X = Cbz or H and Y = D- or L-Leu, in four solvents [water, methanol, acetonitrile, and dimethyl sulfoxide (DMSO)]. An analysis of the tryptophan fluorescence decays using a discrete-exponential model indicates that tryptophan fluorescence decay can be described by a double exponential function in all solvents studied. Lifetime distribution analysis yields a bimodal distribution in protic solvents (water and methanol), whereas an asymmetric, unimodal distribution in an aprotic solvent (DMSO) and uni- or bimodal distributions in acetonitrile solution, depending on leucine configuration. The data are interpreted in terms of the rotamer model, in which the modality and the relative proportions of the lifetime components are related to the population distribution of tryptophan chi(1) rotamers about the C(alpha)--C(beta) bond. The chirality of the Leu(5) residue and solvent properties affect the local environment of the tryptophan residue and therefore influence the distribution of side-chain rotamers. These results are consistent with the results of theoretical conformational calculations.
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Affiliation(s)
- J Malicka
- University of Gdańsk, Faculty of Chemistry, Sobieskiego 18, 80-952 Gdańsk, Poland
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Rzeska A, Malicka J, Stachowiak K, Szymańska A, Łankiewicz L, Wiczk W. Photophysics of phenylalanine analogues. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00394-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nagy PI, Noszál B. Theoretical Study of the Tautomeric/Conformational Equilibrium of Aspartic Acid Zwitterions in Aqueous Solution. J Phys Chem A 2000. [DOI: 10.1021/jp0006227] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter I. Nagy
- Department of Medicinal and Biological Chemistry, The University of Toledo, Toledo, Ohio 43606-3390, and Institute of Pharmaceutical Chemistry, Semmelweis University, H-1092 Budapest, Hungary
| | - Béla Noszál
- Department of Medicinal and Biological Chemistry, The University of Toledo, Toledo, Ohio 43606-3390, and Institute of Pharmaceutical Chemistry, Semmelweis University, H-1092 Budapest, Hungary
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Sillen A, Díaz JF, Engelborghs Y. A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data. Protein Sci 2000; 9:158-69. [PMID: 10739258 PMCID: PMC2144451 DOI: 10.1110/ps.9.1.158] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A method is presented that allows the calculation of the lifetimes of tryptophan residues on the basis of spectral and structural data. It is applied to two different proteins. The calcium binding protein from the sarcoplasm of the muscles of the sand worm Nereis diversicolor (NSCP) changes its conformation upon binding of Ca2+ or Mg2+. NSCP contains three tryptophan residues at position 4, 57, and 170, respectively. The fluorescence lifetimes of W57 are investigated in a mutant in which W4 and W170 have been replaced. The time resolved fluorescence properties of W57 are linked to its different microconformations, which were determined by a molecular dynamics simulation map. Together with the determination of the radiative rate constant from the wavelength of maximum intensity of the decay associated spectra, it was possible to determine an exponential relation between the nonradiative rate constant and the distance between the indole CE3 atom and the carbonyl carbon of the peptide bond reflecting a mechanism of electron transfer as the main determinant of the value for the nonradiative rate constant. This result allows the calculation of the fluorescence lifetimes from the protein structure and the spectra. This method was further tested for the tryptophan of Ha-ras p21 (W32) and for W43 of the Tet repressor, which resulted in acceptable values for the predicted lifetimes.
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Affiliation(s)
- A Sillen
- Laboratory of Biomolecular Dynamics, University of Leuven, Belgium
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27
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Cao X, Fischer G. Infrared Spectral, Structural, and Conformational Studies of Zwitterionic l-Tryptophan. J Phys Chem A 1999. [DOI: 10.1021/jp992421c] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Xiaolin Cao
- Department of Chemistry, The Faculties, The Australian National University, Canberra, ACT 0200, Australia
| | - Gad Fischer
- Department of Chemistry, The Faculties, The Australian National University, Canberra, ACT 0200, Australia
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28
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Brancaleon L, Gasparini G, Manfredi M, Mazzini A. A model for the explanation of the thermally induced increase of the overall fluorescence in tryptophan-X peptides. Arch Biochem Biophys 1997; 348:125-33. [PMID: 9390182 DOI: 10.1006/abbi.1997.0368] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the range of temperature 10-35 degrees C, Trp-X dipeptides show an unusual increase of fluorescence intensity in solution at pH 7. This effect has been recently studied by means of steady-state fluorescence. Although a model involving the deprotonation at the ground state of the zwitterion was proposed, the activation energy for that process could not rule out the involvement of excited state. In order to understand the mechanism of the thermal-induced increase of fluorescence, we present here time-resolved fluorescence experiments on Trp-X and X-Trp dipeptides at different pH and excitation wave-length. The fluorescence lifetimes (tau i) decrease in accord to thermal quenching, with activation energies (Ei) ranging from 4.0 to 6.4 kcal/mol. Under those circumstances where the anomaly was detected the preexponential factors of the longer-lived component increased as well as their fractional fluorescence. This component can be assigned to the anion species. Because of its larger (three- to fourfold) fluorescence quantum yield, compared to that of the corresponding zwitterion, the large increase of the concentration of the anion leads to an increase of the overall emission despite the thermal quenching. Also the decay-associated spectra well account for the red shift of the emission fluorescence spectrum, which accompanies the anomaly. Our model well fits the experimental data using a simple equation which combines Van't Hoff and Arrhenius equations; it also explains the presence of the anomalous thermal quenching exclusively in Trp-X dipeptides excited above 290 nm and at pH around neutrality.
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Affiliation(s)
- L Brancaleon
- Department of Physics, University of Parma, Italy
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29
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Callis PR. 1La and 1Lb transitions of tryptophan: applications of theory and experimental observations to fluorescence of proteins. Methods Enzymol 1997; 278:113-50. [PMID: 9170312 DOI: 10.1016/s0076-6879(97)78009-1] [Citation(s) in RCA: 217] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- P R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman 59717, USA
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30
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Dahms TE, Szabo AG. Conformational heterogeneity in crystalline proteins: time-resolved fluorescence studies. Methods Enzymol 1997; 278:202-21. [PMID: 9170315 DOI: 10.1016/s0076-6879(97)78012-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- T E Dahms
- Department of Biochemistry, University of Ottawa, Ontario, Canada
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31
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32
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van der Spoel D, van Buuren AR, Tieleman DP, Berendsen HJ. Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions. JOURNAL OF BIOMOLECULAR NMR 1996; 8:229-238. [PMID: 8953214 DOI: 10.1007/bf00410322] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Molecular dynamics (MD) simulations of short peptides in water were performed to establish whether it is possible to reproduce experimental data from chemical shift measurements by nuclear magnetic resonance spectroscopy. Three different tetrapeptides were studied. The first, YTGP (Tyr-Thr-Gly-Pro), shows an electrostatic interaction between the aromatic ring of Tyr and the backbone amide hydrogen atom of Gly. The second, YTAP (Tyr-Thr-Ala-Pro), cannot make such an interaction because of steric hindrance of the Ala side chain and hence does not show a well-defined conformation. The third, FTGP (Phe-Thr-Gly-Pro), is shown to alternate between two different conformations. It is demonstrated that small differences in chemical shift, corresponding to these slightly different conformations, can be quantitatively modeled in MD simulations when using the proper force-field parameters and water model Explicit inclusion of hydrogen atoms o the aromatic rings is essential for a proper description of electrostatic interactions, but the choice of the water model is equally important. We found that a combination of the SPC/E water model and a revised GROMOS87 force field gives close agreement with experiment, while the same and other force fields in combination with SPC or TIP3P water did not reproduce the NMR data at all. Simulations of a longer peptide from bovine pancreatic trypsin inhibitor, containing the YTGP sequence, did show the interaction between the aromatic ring and the amide hydrogen, but not as pronounced as the simulations of shorter periods.
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Affiliation(s)
- D van der Spoel
- Bioson Research Institute, University of Groningen, The Netherlands
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33
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Brancaleon L. Time-resolved photoacoustic calorimetry of peptides and proteins containing a single tryptophan. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1996; 398:727-37. [PMID: 8906350 DOI: 10.1007/978-1-4613-0381-7_116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- L Brancaleon
- Dipartimento di Fisica, Universita' di Parma, Italia
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34
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Goldman C, Pascutti PG, Piquini P, Ito AS. On the contribution of electron transfer reactions to the quenching of tryptophan fluorescence. J Chem Phys 1995. [DOI: 10.1063/1.469846] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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35
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Brancaleon L, Crippa PR, Diemmi D. Anomalous temperature fluorescence quenching of N-Trp terminal peptides. Biopolymers 1995; 36:723-33. [PMID: 8555420 DOI: 10.1002/bip.360360606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The photophysics of Trp-containing peptides is extremely affected by the position of the indole ring with respect to substituents. In this work an unusual temperature fluorescence quenching behavior is presented. The N-tryptophan terminal peptides (N-Trp) show an increase of the static emission intensity as rising the temperature from 10 to about 40 degrees C. the anomaly is typical of the N-Trp terminal peptides since neither tryptophan (Trp) nor glycyl-tryptophan (Gly-Trp) and alanyl-tryptophan (Ala-Trp) show the same trend; a similar behavior is not detected in the C-tryptophan terminals. The other important features are the wavelength and pH dependence of the effect. The anomaly is in fact detected only at neutral pH and for excitation wavelength near the red edge of the UVB absorption band of indole. An interpretation of the anomaly is suggested, though more sophisticated techniques are needed to better focus the problem; the model proposed involves the superimposition of a ground state effect (the temperature-induced equilibrium shift from the zwitterionic to the anionic form of the peptides) and an excited state mechanism. At present no unique interpretation can be provided about the excited state mechanism that favors the anomaly ans some suggestions are discussed.
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Affiliation(s)
- L Brancaleon
- Dipartimento di Fisica, Università di Parma, Viale delle Scienze, 43100 Parma, Ilalia
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36
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Kungl AJ, Breitenbach M, Kauffmann HF. Molecular dynamics simulation of the rare amino acid LL-dityrosine and a dityrosine-containing peptide: comparison with time-resolved fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1201:345-52. [PMID: 7803463 DOI: 10.1016/0304-4165(94)90061-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fluorescence of the rare amino acid LL-dityrosine, which is found in insoluble biological materials with structural features, was recently shown to decay non-exponentially (Kungl et al. (1992) J. Fluorescence 2, 63-74). Here we investigated the time-resolved fluorescence of a dityrosine-containing peptide (DCP) to study the influence of side chains on the fluorescence decay of the chromophore. The fluorescence decay of DCP was best fitted by three exponential terms including a sub-nanosecond rise term, the values of which are quite similar to the parameters obtained for the decay of free dityrosine. They were found to depend on the pH of the aqueous solution but not on the temperature. Analysis by an exponential series method revealed broad fluorescence lifetime distributions for DCP. Compared to the corresponding analysis of dityrosine transients, similar lifetime centers were found whereas the widths of the distributions were found broader for DCP. Molecular dyamics (MD) simulations of dityrosine at 300 K show that chi 1 and chi 2 side chain conformers (rotamers) of both tyrosine subunits interconvert on a picosecond timescale. The rates of interconversion were shown to depend critically upon the MD technique applied: in vacuo simulations yielded lower interconversion rates compared to stochastic dynamics (SD) and full MD (water explicitly included). However, MD simulations of the dityrosine-containing peptide revealed no interconversions of the chi 1 and chi 2 side chain rotamers of both tyrosine subunits within a 400 ps trajectory. Interconversions could be induced by raising the temperature of the system (DCP plus solvent) to 340 K. Side chain rotamers of dityrosine are not stable on a fluorescence time scale but are stable when a dityrosine-containing peptide is regarded. Nevertheless both molecules yield similar fluorescence decay patterns. We therefore conclude that the rotamer model proposed for the fluorescence decay of tyrosine and tryptophan cannot be applied to the fluorescence decay of dityrosine and peptides containing this chromophore. This should be of future interest when dityrosine is used as an intrinsic sensor to study complex dityrosine-containing macromolecules by fluorescence spectroscopy.
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Affiliation(s)
- A J Kungl
- Institut für Physikalische Chemie, Universität Wien, Vienna, Austria
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37
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Abstract
The stability mutant Tyr-26-->Asp was studied in the Cro protein from bacteriophage lambda using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 +/- 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1.4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was found to form a capping interaction with the amino terminus of the third alpha-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing helix caps--namely, a model of local unsatisfied hydrogen bonds at the helix termini and the helix macrodipole model. Analysis of the simulations shows that the stabilizing effect of this charged helical cap is due both to favorable hydrogen bonds with backbone NH groups at the helix terminus and to favorable electrostatic interactions (but not hydrogen bonds) with their carbonyls (effectively the next row of local dipoles in the helix). However, electrostatic interactions are weak or negligible with backbone dipolar groups in the helix further away from the terminus. Moreover, the importance of other local electrostatic interactions with polar side chains near the helix terminus, which are neglected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix terminus and other, local preoriented dipolar groups stabilize the helix cap. These findings suggest that similar interactions with preoriented dipolar groups may be important for cooperativity in other charge-dipole interactions and may be employed to advantage for molecular design.
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Affiliation(s)
- B Tidor
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
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38
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Zubkus V, Shamovsky I. Molecular interactions, structure and stability of β-quinol clathrate. Chem Phys Lett 1992. [DOI: 10.1016/0009-2614(92)86125-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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