Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry

被引:66
作者
Chu, FX
Shan, SO
Moustakas, DT
Alber, F
Egea, PF
Stroud, RM
Walter, P
Burlingame, AL
机构
[1] Univ Calif San Francisco, Dept Pharmaceut Chem, Mass Spectrometry Facil, San Francisco, CA 94143 USA
[2] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA
[3] Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA
[4] Univ Calif Berkeley, Joint Grad Grp Bioengn, Berkeley, CA 94720 USA
[5] Univ Calif San Francisco, Dept Biopharmaceut Sci, San Francisco, CA 94143 USA
关键词
computational modeling; protein-protein interactions; protein targeting; GTPases;
D O I
10.1073/pnas.0407456101
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Among the methods used to Unravel protein interaction surfaces, chemical cross-linking followed by identification of the crosslinked peptides by mass spectrometry has proven especially useful in dynamic and complex systems. During the signal recognition particle (SRP)-dependent targeting of proteins to the bacterial plasma membrane, the specific interaction between Ffh (the protein component of SRP) and FtsY (the SRP receptor) is known to be essential for the efficiency and fidelity of this process. In this work, we studied the Escherichia coli and Thermus aquaticus Ffh(.)FtsY complexes by using chemical cross-linking and tandem mass spectrometry to identify nine intermolecular cross-linked peptides. This information was used in conjunction with a previously undescribed model-building approach that combines geometric restraint optimization with macromolecular docking. The resulting model of the Ffh(.)FtsY complex is in good agreement with the crystal structure solved shortly thereafter. Intriguingly, four of the cross-linked pairs involve the M domain of Ffh, which is absent from the crystal structure, providing previously undocumented experimental evidence that the M domain is positioned in close proximity to the Ffh(.)FtsY interface in the complex.
引用
收藏
页码:16454 / 16459
页数:6
相关论文
共 41 条
[1]   Chemical cross-linking and mass spectrometry for protein structural modeling [J].
Back, JW ;
de Jong, L ;
Muijsers, AO ;
de Koster, CG .
JOURNAL OF MOLECULAR BIOLOGY, 2003, 331 (02) :303-313
[2]   Crystal structure of the ribonucleoprotein core of the signal recognition particle [J].
Batey, RT ;
Rambo, RP ;
Lucast, L ;
Rha, B ;
Doudna, JA .
SCIENCE, 2000, 287 (5456) :1232-+
[3]   MODEL FOR SIGNAL SEQUENCE RECOGNITION FROM AMINO-ACID-SEQUENCE OF 54K SUBUNIT OF SIGNAL RECOGNITION PARTICLE [J].
BERNSTEIN, HD ;
PORITZ, MA ;
STRUB, K ;
HOBEN, PJ ;
BRENNER, S ;
WALTER, P .
NATURE, 1989, 340 (6233) :482-486
[4]   Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor [J].
Buskiewicz, I ;
Deuerling, E ;
Gu, SQ ;
Jöckel, J ;
Rodnina, MV ;
Bukau, B ;
Wintermeyer, W .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (21) :7902-7906
[5]   Mapping the signal sequence-binding site on SRP reveals a significant role for the NG domain [J].
Cleverley, RM ;
Gierasch, LM .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (48) :46763-46768
[6]   Mass spectrometry as a tool for protein crystallography [J].
Cohen, SL ;
Chait, BT .
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 2001, 30 :67-85
[7]   Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures [J].
D'Ambrosio, C ;
Talamo, F ;
Vitale, RM ;
Amodeo, P ;
Tell, G ;
Ferrara, L ;
Scaloni, A .
BIOCHEMISTRY, 2003, 42 (15) :4430-4443
[8]   Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry [J].
Dihazi, GH ;
Sinz, A .
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 2003, 17 (17) :2005-2014
[9]   The structure of the potassium channel:: Molecular basis of K+ conduction and selectivity [J].
Doyle, DA ;
Cabral, JM ;
Pfuetzner, RA ;
Kuo, AL ;
Gulbis, JM ;
Cohen, SL ;
Chait, BT ;
MacKinnon, R .
SCIENCE, 1998, 280 (5360) :69-77
[10]   Substrate twinning activates the signal recognition particle and its receptor [J].
Egea, PF ;
Shan, SO ;
Napetschnig, J ;
Savage, DF ;
Walter, P ;
Stroud, RM .
NATURE, 2004, 427 (6971) :215-221