Subnanosecond Motions of Tryptophan Residues in Proteins

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1979 Jan 1

PMID 284374

Citations 65

Authors

I Munro

I Pecht

L Stryer

Affiliations

Soon will be listed here.

Abstract

The dynamics of protein molecules in the subnanosecond and nanosecond time range were investigated by time-resolved fluorescence polarization spectroscopy. Synchrotron radiation from a storage ring was used as a pulsed light source to excite the single tryptophan residue in a series of proteins. The full width at half maximum of the detected light pulse was 0.65 nsec, making it feasible to measure emission anisotropy kinetics in the subnanosecond time range and thereby to resolve internal rotational motions. The proteins investigated exhibit different degrees of rotational freedom of their tryptophan residue, ranging from almost no mobility to nearly complete freedom in the subnanosecond time range. The tryptophan residue of Staphylococcus aureus nuclease B (20,000 daltons) has a single rotational correlation time (varphi) of 9.9 nsec at 20 degrees C, corresponding to a rotation of the whole protein molecule. By contrast, bovine basic A1 myelin protein (18,000 daltons) exhibits varphi of 0.09 and 1.26 nsec, showing that the tryptophan residue in this protein is highly flexible. The single tryptophan of human serum albumin (69,000 daltons) has almost no rotational freedom at 8 degrees C (varphi = 31.4 nsec), whereas at 43 degrees C it rotates rapidly (varphi(1) = 0.14 nsec) within a cone of semiangle 26 degrees in addition to rotating together with the whole protein (varphi(2) = 14 nsec). Of particular interest in the large angular range (semiangle, 34 degrees ) and fast rate (varphi(1) = 0.51 nsec) of the rotational motion of the tryptophan residue in Pseudomonas aeruginosa azurin (14,000 daltons). This residue is known to be located in the hydrophobic interior of the protein. The observed amplitudes and rates of these internal motions of tryptophan residues suggest that elementary steps in functionally significant conformational changes may take place in the subnanosecond time range.

Citing Articles

Role of the Triplet State and Protein Dynamics in the Formation and Stability of the Tryptophan Radical in an Apoazurin Mutant.

Lopez-Pena I, Lee C, Rivera J, Kim J J Phys Chem B. 2022; 126(36):6751-6761.

PMID: 35977067 PMC: 9483921. DOI: 10.1021/acs.jpcb.2c02441.

Photon efficient orientation estimation using polarization modulation in single-molecule localization microscopy.

Thorsen R, Hulleman C, Rieger B, Stallinga S Biomed Opt Express. 2022; 13(5):2835-2858.

PMID: 35774337 PMC: 9203119. DOI: 10.1364/BOE.452159.

Contributions of Conformational Flexibility to High-Affinity Zinc Binding in the Solute Binding Protein AztC.

Serrano F, Yukl E ACS Omega. 2022; 7(4):3768-3774.

PMID: 35128285 PMC: 8811889. DOI: 10.1021/acsomega.1c06639.

F NMR relaxation studies of fluorosubstituted tryptophans.

Lu M, Ishima R, Polenova T, Gronenborn A J Biomol NMR. 2019; 73(8-9):401-409.

PMID: 31435857 PMC: 6878660. DOI: 10.1007/s10858-019-00268-y.

ROSET Model of TonB Action in Gram-Negative Bacterial Iron Acquisition.

Klebba P J Bacteriol. 2016; 198(7):1013-21.

PMID: 26787763 PMC: 4800874. DOI: 10.1128/JB.00823-15.

References

Davis A, MOORE I, Parker D, Taniuchi H . Nuclease B. A possible precursor of nuclease A, an extracellular nuclease of Staphylococcus aureus. J Biol Chem. 1977; 252(18):6544-53. View

Finazzi-Agro A, Rotilio G, Avigliano L, GUERRIERI P, BOFFI V, MONDOVI B . Environment of copper in Pseudomonas fluorescens azurin: fluorometric approach. Biochemistry. 1970; 9(9):2009-14. DOI: 10.1021/bi00811a023. View

Kinosita Jr K, Kawato S, Ikegami A . A theory of fluorescence polarization decay in membranes. Biophys J. 1977; 20(3):289-305. PMC: 1473359. DOI: 10.1016/S0006-3495(77)85550-1. View

Hirshfeld H, Teitelbaum D, Arnon R, Sela M . Basic encephalitogenic protein: A simplified purification on sulphoethyl-sephadex. FEBS Lett. 1970; 7(4):317-320. DOI: 10.1016/0014-5793(70)80193-4. View

Snyder G, Rowan 3rd R, KARPLUS S, Sykes B . Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor. Biochemistry. 1975; 14(17):3765-77. DOI: 10.1021/bi00688a008. View

Brown J . Structural origins of mammalian albumin. Fed Proc. 1976; 35(10):2141-4. View

Mendelson R, Morales M, BOTTS J . Segmental flexibility of the S-1 moiety of myosin. Biochemistry. 1973; 12(12):2250-5. DOI: 10.1021/bi00736a011. View

Yguerabide J, Epstein H, Stryer L . Segmental flexibility in an antibody molecule. J Mol Biol. 1970; 51(3):573-90. DOI: 10.1016/0022-2836(70)90009-4. View

Rosen P, Pecht I . Conformational equilibria accompanying the electron transfer between cytochrome c (P551) and azurin from Pseudomonas aeruginosa. Biochemistry. 1976; 15(4):775-86. DOI: 10.1021/bi00649a008. View

10.

Grinvald A . The use of standards in the analysis of fluorescence decay data. Anal Biochem. 1976; 75(1):260-80. DOI: 10.1016/0003-2697(76)90077-4. View

11.

Eylar E, Caccam J, Jackson J, Westall F, Robinson A . Experimental allergic encephalomyelitis: synthesis of disease-inducing site of the basic protein. Science. 1970; 168(3936):1220-3. DOI: 10.1126/science.168.3936.1220. View

12.

Weber G . Fluorescence-polarization spectrum and electronic-energy transfer in tyrosine, tryptophan and related compounds. Biochem J. 1960; 75:335-45. PMC: 1204430. DOI: 10.1042/bj0750335. View

13.

Yguerabide J . Nanosecond fluorescence spectroscopy of macromolecules. Methods Enzymol. 1972; 26:498-578. DOI: 10.1016/s0076-6879(72)26026-8. View

14.

Belford G, Belford R, Weber G . Dynamics of fluorescence polarization in macromolecules. Proc Natl Acad Sci U S A. 1972; 69(6):1392-3. PMC: 426709. DOI: 10.1073/pnas.69.6.1392. View

15.

Krigbaum W, Hsu T . Molecular conformation of bovine A1 basic protein, a coiling macromolecule in aqueous solution. Biochemistry. 1975; 14(11):2542-6. DOI: 10.1021/bi00682a038. View

16.

Grinvald A, Schlessinger J, Pecht I, Steinberg I . Homogeneity and variability in the structure of azurin molecules studied by fluorescence decay and circular polarization. Biochemistry. 1975; 14(9):1921-29. DOI: 10.1021/bi00680a018. View

17.

Lakowicz J, Weber G . Quenching of protein fluorescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale. Biochemistry. 1973; 12(21):4171-9. PMC: 6945976. DOI: 10.1021/bi00745a021. View

18.

Weber G . Ligand binding and internal equilibria in proteins. Biochemistry. 1972; 11(5):864-78. DOI: 10.1021/bi00755a028. View

19.

Hetzel R, Wuthrich K, Deisenhofer J, Huber R . Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). II. Semi-empirical energy calculations. Biophys Struct Mech. 1976; 2(2):159-80. DOI: 10.1007/BF00863707. View

20.

Hammes G, Wu C . Kinetics of allosteric enzymes. Annu Rev Biophys Bioeng. 1974; 3(0):1-33. DOI: 10.1146/annurev.bb.03.060174.000245. View