A Novel Approach for Assessing Macromolecular Complexes Combining Soft-docking Calculations with NMR Data

Overview

Journal Protein Sci

Specialty Biochemistry

Date 2001 Sep 22

PMID 11567104

Citations 10

Authors

X J Morelli

P N Palma

F Guerlesquin

A C Rigby

Affiliations

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Abstract

We present a novel and efficient approach for assessing protein-protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data collected with heteronuclear single quantum coherence (HSQC) or TROSY nuclear magnetic resonance (NMR) spectroscopy. This method, termed "restrained soft-docking," is validated for several known protein complexes. These data demonstrate that restrained soft-docking extends the size limitations of NMR spectroscopy and provides an alternative method for investigating macromolecular protein complexes that requires less experimental time, effort, and resources. The potential utility of this novel NMR and simulated docking approach in current structural genomic initiatives is discussed.

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References

Wang J, Mauro M, Edwards S, Oatley S, Fishel L, Ashford V . X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis. Biochemistry. 1990; 29(31):7160-73. DOI: 10.1021/bi00483a003. View

Garrett D, Seok Y, Peterkofsky A, Clore G, Gronenborn A . Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry. 1997; 36(15):4393-8. DOI: 10.1021/bi970221q. View

CHERFILS J, Duquerroy S, Janin J . Protein-protein recognition analyzed by docking simulation. Proteins. 1991; 11(4):271-80. DOI: 10.1002/prot.340110406. View

Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser I . Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A. 1992; 89(6):2195-9. PMC: 48623. DOI: 10.1073/pnas.89.6.2195. View

Bacon D, Moult J . Docking by least-squares fitting of molecular surface patterns. J Mol Biol. 1992; 225(3):849-58. DOI: 10.1016/0022-2836(92)90405-9. View

Pelletier H, KRAUT J . Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science. 1992; 258(5089):1748-55. DOI: 10.1126/science.1334573. View

Takahashi H, Nakanishi T, Kami K, Arata Y, Shimada I . A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol. 2000; 7(3):220-3. DOI: 10.1038/73331. View

Morelli X, Dolla A, Czjzek M, Palma P, Blasco F, Krippahl L . Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. Biochemistry. 2000; 39(10):2530-7. DOI: 10.1021/bi992306s. View

Abe Y, Shodai T, Muto T, Mihara K, Torii H, Nishikawa S . Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell. 2000; 100(5):551-60. DOI: 10.1016/s0092-8674(00)80691-1. View

10.

Palma P, Krippahl L, Wampler J, Moura J . BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins. 2000; 39(4):372-84. View

11.

Li M, Spyracopoulos L, Beier N, Putkey J, Sykes B . Interaction of cardiac troponin C with Ca(2+) sensitizer EMD 57033 and cardiac troponin I inhibitory peptide. Biochemistry. 2000; 39(30):8782-90. DOI: 10.1021/bi000473i. View

12.

Clore G . Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization. Proc Natl Acad Sci U S A. 2000; 97(16):9021-5. PMC: 16814. DOI: 10.1073/pnas.97.16.9021. View

13.

Morelli X, Czjzek M, Hatchikian C, Bornet O, Fontecilla-Camps J, Palma N . Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem. 2000; 275(30):23204-10. DOI: 10.1074/jbc.M909835199. View

14.

Guntert P, Salzmann M, Braun D, Wuthrich K . Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR. 2000; 18(2):129-37. DOI: 10.1023/a:1008318805889. View

15.

Mauguen Y, Hartley R, Dodson E, Dodson G, Bricogne G, Chothia C . Molecular structure of a new family of ribonucleases. Nature. 1982; 297(5862):162-4. DOI: 10.1038/297162a0. View

16.

Kuntz I, Blaney J, Oatley S, LANGRIDGE R, Ferrin T . A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982; 161(2):269-88. DOI: 10.1016/0022-2836(82)90153-x. View

17.

Janin J, Wodak S . Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers. 1985; 24(3):509-26. DOI: 10.1002/bip.360240307. View

18.

Louie G, Brayer G . High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c. J Mol Biol. 1990; 214(2):527-55. DOI: 10.1016/0022-2836(90)90197-T. View

19.

Duncan B, Olson A . Shape analysis of molecular surfaces. Biopolymers. 1993; 33(2):231-8. DOI: 10.1002/bip.360330205. View

20.

Jones D, Bycroft M, Lubienski M, Fersht A . Identification of the barstar binding site of barnase by NMR spectroscopy and hydrogen-deuterium exchange. FEBS Lett. 1993; 331(1-2):165-72. DOI: 10.1016/0014-5793(93)80319-p. View