Exploring the nature of the translocon-assisted protein insertion

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 2, 2013, Pages 495-500

  Rychkova, Anna ^a   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Coarse grain modeling; Hydrophobicity scale; Topology

Indexed keywords

ARGININE; TRANSLOCON;

ARTICLE; ENERGY TRANSFER; KINETICS; MEMBRANE BIOLOGY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN PROCESSING; RIBOSOME; TRANSLOCON ASSISTED PROTEIN INSERTION;

BIOPHYSICS; CALCIUM-BINDING PROTEINS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MEMBRANE GLYCOPROTEINS; MEMBRANES; MODELS, MOLECULAR; MUTATION; PROTEIN TRANSPORT; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECEPTORS, PEPTIDE; RIBOSOMES;

EID: 84872194046     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1220361110     Document Type: Article

References (28)

1. Goder V, Spiess M (2003) Molecular mechanism of signal sequence orientation in the endoplasmic reticulum. EMBO J 22(14):3645-3653.
2. Devaraneni PK, et al. (2011) Stepwise insertion and inversion of a type II signal anchor sequence in the ribosome-Sec61 translocon complex. Cell 146(1):134-147.
3. Ojemalm K, Halling KK, Nilsson I, von Heijne G (2012) Orientational preferences of neighboring helices can drive ER insertion of a marginally hydrophobic transmembrane helix. Mol Cell 45(4):529-540.
4. Osborne AR, Rapoport TA, van den Berg B (2005) Protein translocation by the Sec61/ SecY channel. Annu Rev Cell Dev Biol 21:529-550.
5. Zimmer J, Nam YS, Rapoport TA (2008) Structure of a complex of the ATPase SecA and the protein-translocation channel. Nature 455(7215):936-943.
6. Junne T, Schwede T, Goder V, Spiess M (2007) Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. J Biol Chem 282(45):33201-33209.
7. Hessa T, et al. (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433(7024):377-381.
8. Zhang B, Miller TF, 3rd (2010) Hydrophobically stabilized open state for the lateral gate of the Sec translocon. Proc Natl Acad Sci USA 107(12):5399-5404.
9. Gumbart J, Chipot C, Schulten K (2011) Free-energy cost for translocon-assisted insertion of membrane proteins. Proc Natl Acad Sci USA 108(9):3596-3601.
10. Schow EV, et al. (2011) Arginine in membranes: The connection between molecular dynamics simulations and translocon-mediated insertion experiments. J Membr Biol 239(1-2):35-48.
11. Rychkova A, Vicatos S, Warshel A (2010) On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes. Proc Natl Acad Sci USA 107(41):17598-17603.
12. Zhang B, Miller TF, 3rd (2012) Direct simulation of early-stage Sec-facilitated protein translocation. J Am Chem Soc 134(33):13700-13707.
13. Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253(5494):694-698.
14. Kamerlin SCL, Vicatos S, Dryga A, Warshel A (2011) Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu Rev Phys Chem 62:41-64.
15. Hyeon C, Thirumalai D (2011) Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun 2(487):1-11.
16. Zhang B, Miller TF, 3rd (2012) Long-timescale dynamics and regulation of secfacilitated protein translocation. Cell Rep 2(4):927-937.
17. Li LB, Vorobyov I, Allen TW (2008) Potential of mean force and pKa profi le calculation for a lipid membrane-exposed arginine side chain. J Phys Chem B 112(32):9574- 9587.
18. Meindl-Beinker NM, et al. (2006) Asn- and Asp-mediated interactions between transmembrane helices during translocon-mediated membrane protein assembly. EMBO Rep 7:1-6.
19. von Heijne G, Gavel Y (1988) Topogenic signals in integral membrane proteins. Eur J Biochem 174(4):671-678.
20. von Heijne G (1990) The signal peptide. J Membr Biol 115(3):195-201.
21. Schrodinger LLC (2008) The PyMOL Molecular Graphics System. Version 1.2r3pre.
22. Frauenfeld J, et al. (2011) Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nat Struct Mol Biol 18(5):614-621.
23. Hizlan D, et al. (2012) Structure of the SecY complex unlocked by a preprotein mimic. Cell Rep 1(1):21-28.
24. Ismail N, Hedman R, Schiller N, von Heijne G (2012) A biphasic pulling force acts on transmembrane helices during translocon-mediated membrane integration. Nat Struct Mol Biol 19(10):1018-1022.
25. Schutz CN, Warshel A (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44(4):400-417.
26. Goder V, Junne T, Spiess M (2004) Sec61p contributes to signal sequence orientation according to the positive-inside rule. Mol Biol Cell 15(3):1470-1478.
27. Bondar A-N, del Val C, Freites JA, Tobias DJ, White SH (2010) Dynamics of SecY translocons with translocation-defective mutations. Structure 18(7):847-857.
28. Dryga A, Chakrabarty S, Vicatos S, Warshel A (2012) Coarse grained model for exploring voltage dependent ion channels. Biochim Biophys Acta 1818(2):303-317.