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Alston RW, Urbanikova L, Sevcik J, Lasagna M, Reinhart GD, Scholtz JM, Pace CN. Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease Sa. Biophys J 2004; 87:4036-47. [PMID: 15377518 PMCID: PMC1304912 DOI: 10.1529/biophysj.104.050377] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonuclease Sa (RNase Sa) contains no tryptophan (Trp) residues. We have added single Trp residues to RNase Sa at sites where Trp is found in four other microbial ribonucleases, yielding the following variants of RNase Sa: Y52W, Y55W, T76W, and Y81W. We have determined crystal structures of T76W and Y81W at 1.1 and 1.0 A resolution, respectively. We have studied the fluorescence properties and stabilities of the four variants and compared them to wild-type RNase Sa and the other ribonucleases on which they were based. Our results should help others in selecting sites for adding Trp residues to proteins. The most interesting findings are: 1), Y52W is 2.9 kcal/mol less stable than RNase Sa and the fluorescence intensity emission maximum is blue-shifted to 309 nm. Only a Trp in azurin is blue-shifted to a greater extent (308 nm). This blue shift is considerably greater than observed for Trp71 in barnase, the Trp on which Y52W is based. 2), Y55W is 2.1 kcal/mol less stable than RNase Sa and the tryptophan fluorescence is almost completely quenched. In contrast, Trp59 in RNase T1, on which Y55W is based, has a 10-fold greater fluorescence emission intensity. 3), T76W is 0.7 kcal/mol more stable than RNase Sa, indicating that the Trp side chain has more favorable interactions with the protein than the threonine side chain. The fluorescence properties of folded Y76W are similar to those of the unfolded protein, showing that the tryptophan side chain in the folded protein is largely exposed to solvent. This is confirmed by the crystal structure of the T76W which shows that the side chain of the Trp is only approximately 7% buried. 4), Y81W is 0.4 kcal/mol less stable than RNase Sa. Based on the crystal structure of Y81W, the side chain of the Trp is 87% buried. Although all of the Trp side chains in the variants contribute to the unusual positive circular dichroism band observed near 235 nm for RNase Sa, the contribution is greatest for Y81W.
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Affiliation(s)
- Roy W Alston
- Department of Medical Biochemistry and Genetics, Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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De Filippis V, De Boni S, De Dea E, Dalzoppo D, Grandi C, Fontana A. Incorporation of the fluorescent amino acid 7-azatryptophan into the core domain 1-47 of hirudin as a probe of hirudin folding and thrombin recognition. Protein Sci 2004; 13:1489-502. [PMID: 15152084 PMCID: PMC2279979 DOI: 10.1110/ps.03542104] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Revised: 02/17/2004] [Accepted: 02/18/2004] [Indexed: 10/26/2022]
Abstract
7-Azatryptophan (AW), a noncoded isostere of tryptophan (W), possesses interesting spectral properties. In particular, the presence of a nitrogen atom at position 7 in the indolyl nucleus of AW results in a red shift of the absorption maximum and fluorescence emission by 10 and 46 nm, respectively, compared to W. In the present work, we report the chemical synthesis and the conformational and functional characterization of an analog (denoted as Y3AW) of the N-terminal domain 1-47 of hirudin, a highly potent thrombin inhibitor, in which Tyr 3 has been replaced by AW. The results obtained were compared with those of the corresponding Y3W analog. We found that the replacement W --> AW reduces affinity for thrombin by 10-fold, likely because of the lower hydrophobicity of AW compared with that of W. Measurements of the resonance energy transfer effect, which was observed between Tyr13 and the amino acid at position 3 upon disulfide-coupled folding, demonstrate that AW behaves as a better energy acceptor than W for studying protein renaturation. The interaction of Y3AW with thrombin was studied by exciting the sample at 320 nm and recording the change in fluorescence of Y3AW on binding to the enzyme. Our results indicate that the fluorescence of AW of hirudin 1-47 in the Y3AW-thrombin complex is strongly quenched, possibly because of the presence of two structural water molecules at the hirudin-thrombin interface that can promote the nonradiative decay of AW in the excited state. The data herein reported demonstrate that the incorporation of AW can be of broad applicability in the study of protein folding and protein-protein interaction.
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Affiliation(s)
- Vincenzo De Filippis
- Department of Pharmaceutical Sciences, University of Padua, via F. Marzolo 5, I-35131 Padua, Italy.
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Abstract
The genetic code is established by the aminoacylation of transfer RNA, reactions in which each amino acid is linked to its cognate tRNA that, in turn, harbors the nucleotide triplet (anticodon) specific to the amino acid. The accuracy of aminoacylation is essential for building and maintaining the universal tree of life. The ability to manipulate and expand the code holds promise for the development of new methods to create novel proteins and to understand the origins of life. Recent efforts to manipulate the genetic code have fulfilled much of this potential. These efforts have led to incorporation of nonnatural amino acids into proteins for a variety of applications and have demonstrated the plausibility of specific proposals for early evolution of the code.
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Affiliation(s)
- Tamara L Hendrickson
- Department of Chemistry, 1Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA.
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54
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Budisa N, Pal PP, Alefelder S, Birle P, Krywcun T, Rubini M, Wenger W, Bae JH, Steiner T. Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code. Biol Chem 2004; 385:191-202. [PMID: 15101562 DOI: 10.1515/bc.2004.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany.
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55
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Acchione M, Guillemette JG, Twine SM, Hogue CWV, Rajendran B, Szabo AG. Fluorescence based structural analysis of tryptophan analogue-AMP formation in single tryptophan mutants of Bacillus stearothermophilus tryptophanyl-tRNA synthetase. Biochemistry 2004; 42:14994-5002. [PMID: 14674776 DOI: 10.1021/bi0347454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The symmetrical dimer structure of tryptophanyl-tRNA synthetase is similar to that of tyrosyl-tRNA synthetase whose binding behavior and structural details have been elucidated in detail. The structure of both subunits after forming the intermediate tryptophanyl-AMP has important implications for the binding of the cognate tRNA(Trp). Single tryptophan mutants of Bacillus stearothermophilus tryptophanyl-tRNA synthetase have been constructed and expressed and used to probe structural changes in different domains of the enzyme in both subunits. Substrate titrations using the Trp analogues 4-fluorotryptophan and 7-azatryptophan in the presence of ATP to form the corresponding aminoacyl-adenylate reveal significant structural changes occurring throughout the active subunit in regions not confined to the active site. Changes in environment around the specific Trp residues were monitored using UV absorbance and steady-state fluorescence measurements. When titrated with 4-fluorotryptophan, both Trp 91 and Trp 290 fluorescence is quenched (49 and 22%, respectively) when one subunit has formed Trp-AMP. The fluorescence of Trp 48 is enhanced 19%. No further change in signal was observed after a 1:1 dimer/L-4FW-AMP complex ratio had been established. Using an anion-exchange filter binding assay with radiolabeled l-Trp as a substrate, binding to only one subunit was observed under nonsaturating conditions. This agrees with the results of the assay using 7-azatryptophan as a substrate. The observed changes extend to the unfilled subunit where a similar structure is believed to form after one subunit has formed tryptophan-AMP. Movement in the regions of the enzyme containing Trp 290 and Trp 91 suggests a mechanism for cross-subunit communication involving the helical backbone and dimer interface containing these two residues.
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56
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Randall LL, Crane JM, Liu G, Hardy SJS. Sites of interaction between SecA and the chaperone SecB, two proteins involved in export. Protein Sci 2004; 13:1124-33. [PMID: 15010547 PMCID: PMC2280050 DOI: 10.1110/ps.03410104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
SecB, a small tetrameric cytosolic chaperone in Escherichia coli, facilitates the export of precursor poly-peptides by maintaining them in a nonnative conformation and passing them to SecA, which is a peripheral member of the membrane-bound translocation apparatus. It has been proposed by several laboratories that as SecA interacts with various components along the export pathway, it undergoes conformational changes that are crucial to its function. Here we report details of molecular interactions between SecA and SecB, which may serve as conformational switches. One site of interaction involves the final C-terminal 21 amino acids of SecA, which are positively charged and contain zinc. The C terminus of each subunit of the SecA dimer makes contact with the flat beta-sheet that is formed by each dimer of the SecB tetramer. Here we demonstrate that a second interaction exists between the extreme C-terminal alpha-helix of SecB and a site on SecA, as yet undefined but different from the C terminus of SecA. We investigated the energetics of the interactions by titration calorimetry and characterized the hydrodynamic properties of complexes stabilized by both interactions or each interaction singly using sedimentation velocity centrifugation.
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Affiliation(s)
- Linda L Randall
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Columbia, MO 65211, USA.
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57
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Sartori E, Toffoletti A, Corvaja C, Moroder L, Formaggio F, Toniolo C. An oligopeptide doubly labelled with an azulene chromophore and a TEMPO radical. Azulene triplet generation by enhanced ISC from S2. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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58
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Affiliation(s)
- Joachim Weber
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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59
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Hoffmann M, Nemetz C, Madin K, Buchberger B. Rapid translation system: a novel cell-free way from gene to protein. BIOTECHNOLOGY ANNUAL REVIEW 2004; 10:1-30. [PMID: 15504701 DOI: 10.1016/s1387-2656(04)10001-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Proteome research has recently been stimulated by important technological advances in the field of recombinant protein expression. One major breakthrough was the development of a new generation of cell-free transcription/translation systems. The open and flexible character of these systems allows direct control over expression conditions via the addition of supplements to the expression reaction. The possibility of working with linear expression templates instead of cloned plasmids and the ease of downstream processing, circumventing the need for cell-lysis, makes them ideally suited for high-throughput screening applications. Among these novel cell-free systems, the Rapid Translation System (RTS) developed by Roche is the first one that is scalable from micrograms to milligrams of protein. This review describes the basic principles of RTS which differentiate it from traditional in vitro expression technologies, starting from template generation to high-end applications like labeling for structural biology research. Recent results obtained by RTS users from different institutions are presented to illustrate each step of a novel cell-free protein expression workflow and its benefits compared to traditional cell-based expression.
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60
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Perron MJ, Blouse GE, Shore JD. Distortion of the catalytic domain of tissue-type plasminogen activator by plasminogen activator inhibitor-1 coincides with the formation of stable serpin-proteinase complexes. J Biol Chem 2003; 278:48197-203. [PMID: 14500731 DOI: 10.1074/jbc.m306184200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1) is a typical member of the serpin family that kinetically traps its target proteinase as a covalent complex by distortion of the proteinase domain. Incorporation of the fluorescently silent 4-fluorotryptophan analog into PAI-1 permitted us to observe changes in the intrinsic tryptophan fluorescence of two-chain tissue-type plasminogen activator (tPA) and the proteinase domain of tPA during the inhibition reaction. We demonstrated three distinct conformational changes of the proteinase that occur during complex formation and distortion. A conformational change occurred during the initial formation of the non-covalent Michaelis complex followed by a large conformational change associated with the distortion of the proteinase catalytic domain that occurs concurrently with the formation of stable proteinase-inhibitor complexes. Following distortion, a very slow structural change occurs that may be involved in the stabilization or regulation of the trapped complex. Furthermore, by comparing the inhibition rates of two-chain tPA and the proteinase domain of tPA by PAI-1, we demonstrate that the accessory domains of tPA play a prominent role in the initial formation of the non-covalent Michaelis complex.
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Affiliation(s)
- Michel J Perron
- Department of Pathology, Division of Biochemical Research, Henry Ford Health Sciences Center, Detroit, Michigan 48202, USA
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61
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Broos J, Gabellieri E, Biemans-Oldehinkel E, Strambini GB. Efficient biosynthetic incorporation of tryptophan and indole analogs in an integral membrane protein. Protein Sci 2003; 12:1991-2000. [PMID: 12930998 PMCID: PMC2323996 DOI: 10.1110/ps.03142003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Biosynthetic incorporation of tryptophan (Trp) analogs such as 7-azatryptophan, 5-hydroxytryptophan, and fluorotryptophan into a protein can facilitate its structural analysis by spectroscopic techniques such as fluorescence, phosphorescence, nuclear magnetic resonance, and Fourier transform infrared. Until now, the approach has dealt primarily with soluble proteins. In this article, we demonstrate that four different Trp analogs can be very efficiently incorporated into a membrane protein as demonstrated for the mannitol transporter of Escherichia coli (EII(mtl)). EII(mtl) overexpression was under control of the lambdaP(R) promoter, and the E. coli Trp auxotroph M5219 was used as host. This strain constitutively expresses the heat labile repressor protein of the lambdaP(R) promoter. Together with the presence of the repressor gene on the EII(mtl) plasmid, this resulted in a tightly controlled promoter system, a prerequisite for high Trp analog incorporation. A new method for determining the analog incorporation efficiency is presented that is suitable for membrane proteins. The procedure involves fitting of the phosphorescence spectrum as a linear combination of the Trp and Trp analog contributions, taking into account the influence of the protein environment on the Trp analog spectrum. The data show that the analog content of EII(mtl) samples is very high (>95%). In addition, we report here that biosynthetic incorporation of Trp analogs can also be effected with less expensive indole analogs, which in vivo are converted to L-Trp analogs.
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Affiliation(s)
- Jaap Broos
- Department of Biochemistry and Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands.
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62
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Leone M, Rodriguez-Mias RA, Pellecchia M. Selective incorporation of 19F-labeled Trp side chains for NMR-spectroscopy-based ligand-protein interaction studies. Chembiochem 2003; 4:649-50. [PMID: 12851935 DOI: 10.1002/cbic.200300597] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marilisa Leone
- The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92103, USA
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63
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Li Q, Du HN, Hu HY. Study of protein-protein interactions by fluorescence of tryptophan analogs: application to immunoglobulin G binding domain of streptococcal protein G. Biopolymers 2003; 72:116-22. [PMID: 12583014 DOI: 10.1002/bip.10300] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The protein-protein interaction system often contains many fluorophores that may significantly interfere with the quantitative determination of the binding abilities. To solve this perplexing problem, we biosynthetically incorporated the two tryptophan analogs, 5-hydroxytryptophan and 7-azatryptophan, into the immunoglobulin G (IgG) binding domain of streptococcal protein G (PGBD). The exclusive excitation and novel fluorescence changes in both the intensity and anisotropy are beneficial to reporting the details of the interactions between PGBD and the IgG fragments and enable assessment of the binding abilities. The dissociation constants are estimated to be 0.28 microM for the binding of human Fc and 8.0 microM for mouse Fc. The results clearly demonstrate that labeling of tryptophan analogs has very little effect on the binding abilities and is broadly applicable to quantitatively studying protein-protein interactions in a whole biomolecular complex.
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Affiliation(s)
- Qi Li
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
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64
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Affiliation(s)
- Susan M Twine
- Department of Chemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada
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65
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Valencia FF, Paulucci AA, Quaggio RB, Da Silva ACR, Farah CS, Reinach FC. Parallel measurement of Ca2+ binding and fluorescence emission upon Ca2+ titration of recombinant skeletal muscle troponin C. Measurement of sequential calcium binding to the regulatory sites. J Biol Chem 2003; 278:11007-14. [PMID: 12531902 DOI: 10.1074/jbc.m209943200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calcium binding to chicken recombinant skeletal muscle TnC (TnC) and its mutants containing tryptophan (F29W), 5-hydroxytryptophan (F29HW), or 7-azatryptophan (F29ZW) at position 29 was measured by flow dialysis and by fluorescence. Comparative analysis of the results allowed us to determine the influence of each amino acid on the calcium binding properties of the N-terminal regulatory domain of the protein. Compared with TnC, the Ca(2+) affinity of N-terminal sites was: 1) increased 6-fold in F29W, 2) increased 3-fold in F29ZW, and 3) decreased slightly in F29HW. The Ca(2+) titration of F29ZW monitored by fluorescence displayed a bimodal curve related to sequential Ca(2+) binding to the two N-terminal Ca(2+) binding sites. Single and double mutants of TnC, F29W, F29HW, and F29ZW were constructed by replacing aspartate by alanine at position 30 (site I) or 66 (site II) or both. Ca(2+) binding data showed that the Asp --> Ala mutation at position 30 impairs calcium binding to site I only, whereas the Asp --> Ala mutation at position 66 impairs calcium binding to both sites I and II. Furthermore, the Asp --> Ala mutation at position 30 eliminates the differences in Ca(2+) affinity observed for replacement of Phe at position 29 by Trp, 5-hydroxytryptophan, or 7-azatryptophan. We conclude that position 29 influences the affinity of site I and that Ca(2+) binding to site I is dependent on the previous binding of metal to site II.
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Affiliation(s)
- Fernando Fortes Valencia
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, CP 26 077, São Paulo SP CEP 05599-970, Brazil.
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Dunning Hotopp JC, Auchtung TA, Hogan DA, Hausinger RP. Intrinsic tryptophan fluorescence as a probe of metal and alpha-ketoglutarate binding to TfdA, a mononuclear non-heme iron dioxygenase. J Inorg Biochem 2003; 93:66-70. [PMID: 12538054 DOI: 10.1016/s0162-0134(02)00436-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D)/alpha-ketoglutarate (alphaKG) dioxygenase, TfdA, couples the oxidative decarboxylation of alphaKG to the oxidation of the herbicide 2,4-D using a mononuclear non-heme Fe(II) active site. The intrinsic tryptophan fluorescence associated with the four Trp residues in TfdA allows for the use of fluorescence spectroscopy to monitor the binding of iron and alphaKG to the enzyme. The fluorescence spectrum of TfdA is quenched by 50-85% upon addition of Fe(II) or alphaKG, allowing determination of their binding affinities (K(d)=7.45+/-0.61 and 3.35+/-0.35 microM, respectively). Cu, Zn, Mn, Co, Mg, and Ca dictations also quench the TfdA fluorescence with affinities similar to that of Fe(II), whereas monovalent cations such as Na, K, and Li do not. H114A and D116A mutant forms of TfdA, lacking either a histidine or aspartate metallocenter ligand, exhibit weaker affinity for both Fe(II) and alphaKG based on the fluorescence changes. Trp256 is predicted to lie within 5 A of the metal and alphaKG binding sites; however, its substitution by Phe or Leu has negligible effects on the Fe(II)- and alphaKG-dependent fluorescence quenching. Because Trp195 is predicted to be quite distant ( approximately 15 A) from the active site, we conclude that some combination of Trp113 and Trp248 serves as the reporter that senses metal and cofactor binding to TfdA.
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Affiliation(s)
- Julie C Dunning Hotopp
- Department of Microbiology and Molecular Genetics, 160 Giltner Hall, Michigan State University, East Lansing, MI 48824, USA
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67
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Formaggio F, Sartori E, Toffoletti A, Corvaja C, Moroder L, Toniolo C. Interaction of 7-Azatryptophan and ß-(1-Azulenyl)-Alanine with a Nitroxyl Radical. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 527:731-7. [PMID: 15206796 DOI: 10.1007/978-1-4615-0135-0_86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Aal and 7-Atrp, quasi-isosteric with Trp, have been inserted together with a TOAC residue in two 3(10)-helical, model hexapeptides. The interaction of photoexcited AA1 and 7-Atrp with the nitroxide group of TOAC was investigated by time resolved EPR. Both peptides showed nitroxide spin polarized signals revealing that an intramolecular interaction takes places between the excited chromophore and the free radical moiety. The observation of a spin polarized signal in emission for AA1 is accounted for by the formation of triplet azulene by radical promoted enhanced inter system crossing (EISC).
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy
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68
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Ma K, Wang K. Interaction of nebulin SH3 domain with titin PEVK and myopalladin: implications for the signaling and assembly role of titin and nebulin. FEBS Lett 2002; 532:273-8. [PMID: 12482578 DOI: 10.1016/s0014-5793(02)03655-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Skeletal muscle nebulin is thought to determine thin filament length and regulate actomyosin interaction in a calcium/calmodulin or S100 sensitive manner. We have investigated the binding of nebulin SH3 with proline-rich peptides derived from the 28-mer PEVK modules of titin and the Z-line protein myopalladin, using fluorescence, circular dichroism and nuclear magnetic resonance techniques. Of the six peptides studied, PR2 of titin (VPEKKAPVAPPK) and myopalladin MyoP2 (646VKEPPPVLAKPK657) bind to nebulin SH3 with micromolar affinity (approximately 31 and 3.4 microM, respectively), whereas the other four peptides bind weakly (>100 microM). Sequence analysis of titins reveals numerous SH3 binding motifs that are highly enriched in the PEVK segments of titin isoforms. Our findings suggest that titin PEVK and myopalladin may play signaling roles in targeting and orientating nebulin to the Z-line during sarcomere assembly.
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Affiliation(s)
- Kan Ma
- Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, B50/Rm 1140, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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69
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Twine SM, Murphy L, Phillips RS, Callis P, Cash MT, Szabo AG. The Photophysical Properties of 6-Azaindole. J Phys Chem B 2002. [DOI: 10.1021/jp027102r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susan M. Twine
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Lise Murphy
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Robert S. Phillips
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Patrik Callis
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Michael T. Cash
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
| | - Arthur G. Szabo
- Department of Chemistry, Wilfrid Laurier University, 75 University Ave., Waterloo, Ontario N2L 3C5, Canada, Departments of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, and Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717
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70
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Adams PD, Chen Y, Ma K, Zagorski MG, Sönnichsen FD, McLaughlin ML, Barkley MD. Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc 2002; 124:9278-86. [PMID: 12149035 DOI: 10.1021/ja0167710] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intramolecular quenching of tryptophan fluorescence by protein functional groups was studied in a series of rigid cyclic hexapeptides containing a single tryptophan. The solution structure of the canonical peptide c[D-PpYTFWF] (pY, phosphotyrosine) was determined in aqueous solution by 1D- and 2D-(1)H NMR techniques. The peptide backbone has a single predominant conformation. The tryptophan side chain has three chi(1) rotamers: a major chi(1) = -60 degrees rotamer with a population of 0.67, and two minor rotamers of equal population. The peptides have three fluorescence lifetimes of about 3.8, 1.8, and 0.3 ns with relative amplitudes that agree with the chi(1) rotamer populations determined by NMR. The major 3.8-ns lifetime component is assigned to the chi(1) = -60 degrees rotamer. The multiple fluorescence lifetimes are attributed to differences among rotamers in the rate of excited-state electron transfer to peptide bonds. Electron-transfer rates were calculated for the six preferred side chain rotamers using Marcus theory. A simple model with reasonable assumptions gives excellent agreement between observed and calculated lifetimes for the 3.8- and 1.8-ns lifetimes and assigns the 1.8-ns lifetime component to the chi(1) = 180 degrees rotamer. Substitution of phenylalanine by lysine on either side of tryptophan has no effect on fluorescence quantum yield or lifetime, indicating that intramolecular excited-state proton transfer catalyzed by the epsilon-ammonium does not occur in these peptides.
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Affiliation(s)
- Paul D Adams
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, USA
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71
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Abstract
SecA, a homodimeric protein involved in protein export in Escherichia coli, exists in the cell both associated with the membrane translocation apparatus and free in the cytosol. SecA is a multifunctional protein involved in protein localization and regulation of its own expression. To carry out these functions, SecA interacts with a variety of proteins, phospholipids, nucleotides, and nucleic acid and shows two enzymic activities. It is an ATPase and a helicase. Its role during protein localization involves interaction with the precursor polypeptides to be exported, the cytosolic chaperone SecB, and the SecY subunit of the membrane-associated translocase, as well as with acidic phospholipids. At the membrane, SecA undergoes a cycle of binding and hydrolysis of ATP coupled to conformational changes that result in translocation of precursors through the cytoplasmic membrane. The helicase activity of SecA and its affinity for its mRNA are involved in regulation of its own expression. SecA has been reported to exist in at least two conformational states during its functional cycle. Here we have used analytical centrifugation, as well as column chromatography coupled with multi-angle light scatter, to show that in solution SecA undergoes at least two monomer-dimer equilibrium reactions that are sensitive to temperature and to concentration of salt.
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Affiliation(s)
- Ronald L Woodbury
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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72
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Brennan JD, Capretta A, Yong K, Gerritsma D, Flora KK, Jones A. Sensitization of lanthanides by nonnatural amino acids. Photochem Photobiol 2002; 75:117-21. [PMID: 11883598 DOI: 10.1562/0031-8655(2002)075<0117:solbna>2.0.co;2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The sensitization of Eu(III) and Tb(III) by ethylenediaminetetraaceticacid (EDTA)-derivatized tryptophan (Trp), 7-azatryptophan (7AW) and 5-hydroxytryptophan (5HW) has been examined. These Trp analogs were utilized in the present study because they can be incorporated into proteins in place of native Trp residues and because they absorb strongly beyond 305 nm (where Trp absorbance goes to zero), allowing selective excitation of such species in the presence of other Trp-containing proteins. All three indole derivatives were able to sensitize Tb(III) luminescence, with the relative sensitization being in the order Trp > 5HW > 7AW. On the other hand, only the 7AW-EDTA complex was able to sensitize Eu(III) luminescence, likely owing to a better spectral overlap between 7AW emission and Eu(III) absorbance. The sensitized emission of Tb(III) and Eu(II) displayed the expected long emission lifetimes at 545 nm [for Tb(III)] and 617 nm [for Eu(III)], indicating that long-lifetime lanthanide emission could be produced using nonnatural amino-acid donors. Thus, 7AW- and 5HW-sensitized lanthanide emissions should prove to be useful in biophysical studies, such as the use of fluorescence energy transfer to probe biomolecular interactions in vivo.
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Affiliation(s)
- John D Brennan
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.
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73
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Senear DF, Mendelson RA, Stone DB, Luck LA, Rusinova E, Ross JBA. Quantitative analysis of tryptophan analogue incorporation in recombinant proteins. Anal Biochem 2002; 300:77-86. [PMID: 11743694 DOI: 10.1006/abio.2001.5441] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three different methods to quantitate tryptophan (Trp) analogue incorporation into recombinant proteins are described: first, spectroscopic analysis based on a linear combination of the absorption spectra of the aromatic residues in the denatured Trp-containing or analogue-substituted protein; second, chromatographic separation of analogue-substituted and Trp-containing proteins by HPLC; and third, mass spectrum analysis of the mixture of analogue-substituted and Trp-containing proteins. An accurate estimate of analogue incorporation in single-Trp proteins can be obtained directly by either analysis of the absorption spectrum or HPLC chromatography. While analysis of the absorption spectrum or HPLC chromatogram can provide an assessment of the average level of analogue incorporation for proteins that contain two or more Trp residues, mass spectroscopy analysis of peptides generated by protease digestion and separated by HPLC provides a general method for a complete quantitative description of the distribution of analogue incorporation. The more complex analysis by mass spectroscopy becomes important for multi-Trp proteins because the distribution of analogue versus Trp-containing polypeptide chains may not be the same as that predicted on the basis of average level of analogue incorporation.
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Affiliation(s)
- Donald F Senear
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697, USA
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74
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Engelborghs Y. The analysis of time resolved protein fluorescence in multi-tryptophan proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:2255-2270. [PMID: 11603842 DOI: 10.1016/s1386-1425(01)00485-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the last decades, considerable progress has been made in the analysis of the fluorescence decay of proteins with more than one tryptophan. The construction of single tryptophan containing proteins has shown that the lifetimes of the wild type proteins are often the linear combinations of the family lifetimes of the contributing tryptophan residues. Additivity is not followed when energy transfer takes place among tryptophan residues or when the structure of the remaining protein is altered upon the modification. Progress has also been made in the interpretation of the value of the lifetime and the linkage with the immediate environment. Probably all the irreversible processes leading to return to the ground state have been catalogued and their rate constants are documented. Also, the process of electron transfer to the peptide carbonyl is becoming more and more documented and is linked to the rotameric state of tryptophan. Reversible excited state processes are also being considered, including reversible interconversions between rotamers. Interesting information about tryptophan and its environment comes also from anisotropy measurements for proteins in the native, the denatured and the molten globule states. Alterations of protein fluorescence due to the effects of ligand binding or side chain modifications can be analyzed via the ratio of the quantum yields of the modified protein and the reference state. Using the ratio of quantum yields and the (amplitude weighted) average lifetime, three factors can be identified: (1) a change in the apparent radiative rate constant reflecting either static quenching or an intrinsic change in the radiative properties; (2) a change in dynamic quenching; and (3) a change in the balance of the populations of the microstates or local static quenching.
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Affiliation(s)
- Y Engelborghs
- Laboratory of Biomolecular Dynamics, University of Leuven, Belgium.
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75
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Berger MD, Lee AM, Simonette RA, Jackson BE, Roca AI, Singleton SF. Design and evaluation of a tryptophanless RecA protein with wild type activity. Biochem Biophys Res Commun 2001; 286:1195-203. [PMID: 11527427 DOI: 10.1006/bbrc.2001.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C-terminal domain of the Escherichia coli RecA protein contains two tryptophan residues whose native fluorescence emission provides an interfering background signal when other fluorophores such as 1,N(6)-ethenoadenine, 2-aminopurine and other tryptophan residues are used to probe the protein's activities. Replacement of the wild type tryptophans with nonfluorescent residues is not trivial because one tryptophan is highly conserved and the C-terminal domain functions in both DNA binding as well as interfilament protein-protein contact. We undertook the task of creating a tryptophanless RecA protein with WT RecA activity by selecting suitable amino acid replacements for Trp290 and Trp308. Mutant proteins were screened in vivo using assays of SOS induction and cell survival following UV irradiation. Based on its activity in these assays, the W290H-W308F W-less RecA was purified for in vitro characterization and functioned like WT RecA in DNA-dependent ATPase and DNA strand exchange assays. Spectrofluorometry indicates that the W290H-W308F RecA protein generates no significant emission when excited with 295-nm light. Based on its ability to function as wild type protein in vivo and in vitro, this dark RecA protein will be useful for future fluorescence experiments.
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Affiliation(s)
- M D Berger
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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76
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Budisa N, Alefelder S, Bae JH, Golbik R, Minks C, Huber R, Moroder L. Proteins with beta-(thienopyrrolyl)alanines as alternative chromophores and pharmaceutically active amino acids. Protein Sci 2001; 10:1281-92. [PMID: 11420430 PMCID: PMC2374119 DOI: 10.1110/ps.51601] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
L-beta-(Thieno[3,2-b]pyrrolyl)alanine and L-beta-(thieno[2,3-b]pyrrolyl)alanine are mutually isosteric and pharmaceutically active amino acids that mimic tryptophan with the benzene ring in the indole moiety replaced by thiophene. Sulfur as a heteroatom causes physicochemical changes in these tryptophan surrogates that bring about completely new properties not found in the indole moiety. These synthetic amino acids were incorporated into recombinant proteins in response to the Trp UGG codons by fermentation in a Trp-auxotrophic Escherichia coli host strain using the selective pressure incorporation method. Related protein mutants expectedly retain the secondary structure of the native proteins but show significantly changed optical and thermodynamic properties. In this way, new spectral windows, fluorescence, polarity, thermodynamics, or pharmacological properties are inserted into proteins. Such an engineering approach by translational integration of synthetic amino acids with a priori defined properties, as shown in this study, proved to be a novel and useful tool for protein rational design.
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Affiliation(s)
- N Budisa
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany.
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77
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Bae JH, Alefelder S, Kaiser JT, Friedrich R, Moroder L, Huber R, Budisa N. Incorporation of beta-selenolo[3,2-b]pyrrolyl-alanine into proteins for phase determination in protein X-ray crystallography. J Mol Biol 2001; 309:925-36. [PMID: 11399069 DOI: 10.1006/jmbi.2001.4699] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
beta-Selenolo[3,2-b]pyrrolyl-L-alanine that mimics tryptophan with the benzene ring of the indole moiety replaced by selenophene, was incorporated into human annexin V and barstar. This was achieved by fermentation and expression in a Trp-auxotrophic Escherichia coli host strain using the selective pressure incorporation method. The seleno- proteins were obtained in yields comparable to those of the wild-type proteins and exhibit full crystallographic isomorphism to the parent proteins, but expectedly show altered absorbance profiles and quenched tryptophan fluorescence. Since the occurrence of tryptophan residues in proteins is rare, incorporation of the electron-rich selenium-containing tryptophan surrogate into proteins represents a useful supplementation and even a promising novel alternative to selenomethionine for solving the phase problem in protein X-ray crystallography.
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Affiliation(s)
- J H Bae
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, 82152, Martinsried, Germany
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78
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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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79
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Minks C, Alefelder S, Moroder L, Huber R, Budisa N. Towards New Protein Engineering: In Vivo Building and Folding of Protein Shuttles for Drug Delivery and Targeting by the Selective Pressure Incorporation (SPI) Method. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00827-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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80
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Vincent M, Gilles AM, Li de la Sierra IM, Briozzo P, Bârzu O, Gallay J. Nanosecond Fluorescence Dynamic Stokes Shift of Tryptophan in a Protein Matrix. J Phys Chem B 2000. [DOI: 10.1021/jp000638x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michel Vincent
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Anne-Marie Gilles
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Inès M. Li de la Sierra
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Pierre Briozzo
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Octavian Bârzu
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
| | - Jacques Gallay
- LURE Bâtiment 209D, UMR 130 CNRS, Université Paris-Sud, 91898 Orsay Cedex, France, and Laboratoire de Chimie Structurale des Macromolécules, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Biochimie Structurale, URA 1129 CNRS, Institut Pasteur, 75724 Paris Cedex 15, France, and Laboratoire de Chimie Biologique, U206 INRA Paris-Grignon, 78850 Thiverval-Grignon, France
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81
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Minks C, Huber R, Moroder L, Budisa N. Noninvasive tracing of recombinant proteins with "fluorophenylalanine-fingers". Anal Biochem 2000; 284:29-34. [PMID: 10933852 DOI: 10.1006/abio.2000.4667] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-level residue-specific replacement of phenylalanine residues in recombinant human annexin V and azurin from Pseudomonas aeruginosa with o-fluorophenylalanine, m-fluorophenylalanine, and p-fluorophenylalanine has been achieved using the selective pressure incorporation method. Incorporation was confirmed analytically and by UV spectroscopy while the secondary and tertiary structures of these protein mutants in solution remained unchanged upon the effected substitutions. Fluorinated phenylalanines alone and when integrated into proteins exhibit two characteristic and prominent shoulders ("fingers") in the UV spectrum in the range of 260-270 nm, which do not overlap with the contributions of tyrosine and tryptophan residues in the protein UV spectra. Thus, the presence of such "fluorophenylalanine fingers" ("FF fingers") opens a new spectral window to identify the labeled target protein among other nonlabeled cellular proteins in preparative work by simple UV spectroscopy. In the coming era of proteomics such a reliable, cheap, and easy reproducible methodology might have a great potential for speeding up the identification and characterization of target molecules in the total protein output from the genomes of a variety of organisms.
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Affiliation(s)
- C Minks
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, Martinsried, D-82152, Germany
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82
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Lanfermeijer FC, Detmers FJ, Konings WN, Poolman B. On the binding mechanism of the peptide receptor of the oligopeptide transport system of Lactococcus lactis. EMBO J 2000; 19:3649-56. [PMID: 10899119 PMCID: PMC313990 DOI: 10.1093/emboj/19.14.3649] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lactococcus lactis degrades exogenous proteins such as beta-casein to peptides of 4-30 amino acids, and uses these as nitrogen sources. The binding protein or receptor (OppA(Ll)) of the oligopeptide transport system (Opp) of L.LACTIS: has the unique capacity to bind peptides from five up to at least 20 residues. To study the binding mechanism of OppA(Ll), nonameric peptides were used in which the cysteine at position 1, 3, 4, 5, 6, 7 or 9 was selectively labeled with either bulky and non-fluorescent or bulky and fluorescent groups. Also, nonameric peptides with a non-natural residue, azatryptophan, at positions 3 or 7 were used. The fluorescence of azatryptophan reports on the polarity of the environment. The studies indicate that the binding protein encloses the first six amino acids of the peptide, whereas the remaining residues stick out and interact with the surface of the binding protein. The peptide binding mechanism of OppA(Ll) is discussed in relation to known three-dimensional structures of members of this class of proteins, and an adaptation of the general binding mechanism is proposed.
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Affiliation(s)
- F C Lanfermeijer
- Departments of Microbiology and Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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83
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Greene MK, Steede NK, Landry SJ. Domain-specific spectroscopy of 5-hydroxytryptophan-containing variants of Escherichia coli DnaJ. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1480:267-77. [PMID: 10899627 DOI: 10.1016/s0167-4838(00)00078-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tryptophan-containing variants of Escherichia coli DnaJ protein were constructed in order to examine the hypothetical domain structure by fluorescence quenching and denaturant-induced unfolding. Two residues in the J-domain and one in the Gly/Phe-rich region were targeted for replacement and the proteins were expressed in a tryptophan auxotrophic strain in the presence of 5-hydroxytryptophan (5-HW). Fluorescence quenching with iodide of 5-HW in the variant proteins suggests that the Gly/Phe-rich region is more accessible to solvent than the J-domain. This is consistent with the proposal that the Gly/Phe-rich region is unstructured. Unfolding of the 5-HW-containing variants was monitored by fluorescence, and the results showed that the unfolding of the J-domain is cooperative and the unfolding of the Gly/Phe-rich region is not cooperative.
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Affiliation(s)
- M K Greene
- Department of Biochemistry (SL43), Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112-2699, USA
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84
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Liu B, Barkley MD, Morales GA, McLaughlin ML, Callis PR. Fluorescence Properties of Benz[f]indole, a Wavelength and Quenching Selective Tryptophan Analog. J Phys Chem B 2000. [DOI: 10.1021/jp9925536] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | | | - Patrik R. Callis
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717
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85
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Zemsky J, Rusinova E, Nemerson Y, Luck LA, Ross JA. Probing local environments of tryptophan residues in proteins: Comparison of19F nuclear magnetic resonance results with the intrinsic fluorescence of soluble human tissue factor. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19991201)37:4<709::aid-prot19>3.0.co;2-v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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86
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Scott DJ, Leejeerajumnean S, Brannigan JA, Lewis RJ, Wilkinson AJ, Hoggett JG. Quaternary re-arrangement analysed by spectral enhancement: the interaction of a sporulation repressor with its antagonist. J Mol Biol 1999; 293:997-1004. [PMID: 10547280 DOI: 10.1006/jmbi.1999.3221] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein/protein interaction between SinI and SinR has been studied by analytical ultracentrifugation and gel electrophoresis in an attempt to understand how these proteins contribute to developmental control of sporulation in Bacillus subtilis. SinR was found to be tetrameric, while SinI was found to exist as monomers and dimers in a rapidly reversible equilibrium. Labelling of SinR by incorporating the tryptophan analogue 7-azatryptophan (7AW) into the protein in place of tryptophan shifts the UV absorbance spectrum, thus allowing selective monitoring of 7AWSinR at 315 nm using the UV absorption optics of the analytical ultracentrifuge. Selective monitoring of SinR in mixtures of SinR and SinI enables the binding and stoichiometry of the interaction to be investigated quantitatively and unambiguously. We demonstrate that the oligomeric forms of SinR and SinI re-arrange to form a tight 1:1 SinR:SinI complex, with no stable intermediate species. A fragment of SinR, SinR(1-69), which contains only the DNA-binding domain, was found to be monomeric, showing that the protein appears not to oligomerise in a similar manner to the Cro repressor, a protein with which it shares a marked structural similarity.
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Affiliation(s)
- D J Scott
- Department of Biology, University of York, Heslington, UK
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87
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Das K, Ashby KD, Smirnov AV, Reinach FC, Petrich JW, Farah CS. Fluorescence Properties of Recombinant Tropomyosin Containing Tryptophan, 5-Hydroxytryptophan and 7-Azatryptophan. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb08275.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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88
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89
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McCaul CP, Ludescher RD. Room Temperature Phosphorescence from Tryptophan and Halogenated Tryptophan Analogs in Amorphous Sucrose. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb07985.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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90
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Sydor JR, Herrmann C, Kent SB, Goody RS, Engelhard M. Design, total chemical synthesis, and binding properties of a [Leu-91-N1-methyl-7-azaTrp]Ras-binding domain of c-Raf-1. Proc Natl Acad Sci U S A 1999; 96:7865-70. [PMID: 10393913 PMCID: PMC22153 DOI: 10.1073/pnas.96.14.7865] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Ras-binding domain (RBD) of c-Raf-1 has been synthesized chemically, taking advantage of the chemical ligation of two peptide fragments of the protein. This procedure allowed incorporation of an unnatural amino acid (N1-methyl-7-azatryptophan) at position 91 of RBD, producing a protein with fluorescent properties distinct from and distinguishable from those of proteins containing the natural fluorophore tryptophan. The resulting protein was shown to interact with Ras in a manner that was almost indistinguishable from that of unmodified RBD based on transient kinetic monitoring of the binding event. Modified RBD containing the L-isomer of the unnatural amino acid or its racemic D,L mixture appeared to interact identically with Ras. The approach demonstrates a general procedure for the introduction of unnatural amino acids that can be used for monitoring protein-protein interactions and for the introduction of an unnatural backbone structure at strategic positions.
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Affiliation(s)
- J R Sydor
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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91
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Budisa N, Minks C, Alefelder S, Wenger W, Dong F, Moroder L, Huber R. Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J 1999; 13:41-51. [PMID: 9872928 DOI: 10.1096/fasebj.13.1.41] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The high precision and fidelity of the genetic message transmission are ensured by numerous proofreading steps, from DNA replication and transcription to protein translation. The key event for translational fidelity is the proper codon assignment for 20 canonical amino acids. An experimental codon reassignment is possible for noncanonical amino acids in vivo using artificially constructed expression hosts under efficient selective pressure. However, such amino acids may interfere with the cellular metabolism and thus do not belong to the 'first' or 'restricted' part of the universal code, but rather to a second or 'relaxed' part, which is limited mainly by the downstream proofreading in the natural translational machinery. Correspondingly, not all possible alpha-amino acids can be introduced into proteins. The aim of this study is to discuss biological and evolutionary constraints on possible candidates for this second coding level of the universal code. Engineering of such a 'second' code is expected to have great academic as well as practical impact, ranging from protein folding studies to biomedicine.
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Affiliation(s)
- N Budisa
- Max Planck Institut für Biochemie, D-82152 Martinsried, Germany.
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92
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Synthesis of (2S)-2-amino-3-(1H-4-indolyl)propanoic acid, a novel tryptophan analog for structural modification of bioactive peptides. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0957-4166(98)00445-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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93
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Senear DF, Ross JB, Laue TM. Analysis of protein and DNA-mediated contributions to cooperative assembly of protein-DNA complexes. Methods 1998; 16:3-20. [PMID: 9774512 DOI: 10.1006/meth.1998.0641] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The cooperative assembly of protein-DNA complexes is a widespread phenomenon that is of particular significance to transcriptional regulation. Assembly of these complexes is controlled by the chemistry of the macromolecular interactions. In this sense, transcriptional regulation is a chemical issue. The purpose of this review is to present an analytical approach designed to understand this regulation from a chemical perspective. By investigating the solution interactions between all combinations of molecules, protein-protein, protein-ligand, and protein-DNA, and the interplay between them, it is possible to determine the relative free energies of the different configurations of the regulatory complex. This governs their distribution and thereby controls the biological activity. To illustrate the approach, we will address the molecular basis for cooperativity in the bacteriophage lambda, lysogenic-lytic switch mechanism, a system that has long served as a paradigm for gene regulation. The driving force for cooperativity in the assembly of gene regulatory complexes is generally thought to be provided by direct protein-protein interactions. However, other interactions mediated by both proteins and DNA are also involved and may be critical to the regulatory mechanism. We will review advances over the past several years in the application of biophysical chemical methods to investigate protein-protein and protein-DNA interactions. Many of these applications were first employed for the lambda system. In addition to describing the physical basis for the methods, we will focus on the unique information that can be gained and how to combine the information obtained from several techniques to develop a comprehensive view of the critical regulatory interactions.
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Affiliation(s)
- D F Senear
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California, 92697, USA. dfsenear.uci.edu
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94
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Cioni P, Erijman L, Strambini GB. Phosphorescence emission of 7-azatryptophan and 5-hydroxytryptophan in fluid solutions and in alpha2 RNA polymerase. Biochem Biophys Res Commun 1998; 248:347-51. [PMID: 9675138 DOI: 10.1006/bbrc.1998.8939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The tryptophan analogues 7-azaindole (7-Aza W) and 5-hydroxytryptophan (5-OH W) have a significant absorbance between 310-320 nm, which allows them to act as selective luminescence probes in protein mixtures containing a large number of tryptophan residues. To assess the potential of their phosphorescence emission in probing the nature of protein environments the delayed emission was examined as a function of temperature and solvent viscosity. Whereas in low temperature (135 K) propylene glycol/buffer glasses the phosphorescence of both 7-aza W and 5-OH W is structured, intense and exhibit a lifetime of a few seconds, above the glass transition temperature (180 K) the delayed emission is considerably quenched. Temperature profiles show that as the solvent is more fluid the phosphorescence of 5-OH W becomes red shifted, poorly structured and the triplet lifetime drops steeply reaching 29 micro(s) in buffer at 274 K. For 7-aza W the alterations are more drastic and no phosphorescence could be detected above 193 K. This implies that in fluid aqueous media the excited triplet state of these analogues is deactivated by vary efficient nonradiative processes. The quenching of 5-OH phosphorescence is not prevented even when the chromophore is inserted in a solvent protected protein environment. Indeed, substitution of the single Trp of a2 RNA Polymerase, which according to its relatively low phosphorescence lifetime at ambient temperature is substantially shielded from the solvent, with 5-OH did not inhibit the quenchability of the latter. Knowledge of the quenching mechanisms is therefore needed for this emission to report on the nature of the protein environment.
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Affiliation(s)
- P Cioni
- C.N.R. - Istituto di Biofisica, Via S. Lorenzo, 26, Pisa, 56127, Italy.
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95
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Ozarowski A, Wu JQ, Maki AH. Study of complexes of a tryptophan-free mutant of E. coli trp aporepressor with tryptophan analogues using optically detected magnetic resonance (ODMR). FEBS Lett 1998; 422:52-6. [PMID: 9475168 DOI: 10.1016/s0014-5793(97)01602-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phosphorescence and optically detected magnetic resonance (ODMR) spectra of tryptophan (W) and several of its analogues (4-, 5-, 6-methyltryptophan (MeW); 4-, 5-, 6-fluorotryptophan (FW); 5-bromotryptophan) are compared with those of complexes formed with the W-free trp aporepressor from Escherichia coli (W19,99F). W19,99F binds W and each analogue except 4-FW with an estimated KD < or = 30 microM; triplet state spectroscopic and kinetic effects that accompany binding at the corepressor site are reported. ODMR data for the MeW isomers are presented for the first time. No binding of 7-azaW is observed, in agreement with the low affinity found by previous workers.
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Affiliation(s)
- A Ozarowski
- Department of Chemistry, University of California, Davis 95616, USA
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96
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Driscoll SL, Hawkins ME, Balis FM, Pfleiderer W, Laws WR. Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides. Biophys J 1997; 73:3277-86. [PMID: 9414238 PMCID: PMC1181229 DOI: 10.1016/s0006-3495(97)78352-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The fluorescence properties of 3-methyl-isoxanthopterin (3-MI) incorporated into different oligonucleotides have been determined. This highly fluorescent guanosine analog has its absorption and fluorescence spectra well resolved from those of the normal nucleotides and the aromatic amino acids. The small shifts observed in absorption and fluorescence emission spectra upon incorporation of 3-MI into these oligonucleotides are consistent with a general solvent effect and do not suggest any contribution from the position of the probe from the 5' end, the sequence of nucleotides immediately 5' or 3' to the probe, or the single- or double-stranded nature of the oligomer. However, steady-state and time-resolved fluorescence studies indicate that the presence of a purine immediately 5' or 3' to the probe results in some dynamic but mostly static quenching in the single-stranded oligomer. Furthermore, a 3' purine is more effective than a 5' purine, and an adenine appears to be more effective than a guanine for these static quenching interactions. Formation of the double-stranded oligomer leads to an additional loss of quantum yield, which can also be ascribed primarily to static quenching. These results show that this new class of spectrally enhanced fluorescent purine analogs will be able to provide useful information concerning the perturbation of nucleic acid structures.
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Affiliation(s)
- S L Driscoll
- Department of Biochemistry, Mount Sinai School of Medicine, New York, New York 10029, USA
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