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McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585-590
Mears JA, Cannone JJ, Stagg SM, Gutell RR, Agrawal RK, Harvey SC (2002) Modeling a mini-
mal ribosome based on comparative sequence analysis. J Mol Biol 321:215-234
Meskauskas A, Dinman JD (2007) Ribosomal protein L3: gatekeeper to the A site. Mol Cell
25:877-888
Moazed D, Noller HF (1989) Intermediate states in the movement of transfer RNA in the ribo-
some. Nature 342:142-148
Munro JB, Altman RB, O'Connor N, Blanchard SC (2007) Identification of two distinct hybrid
state intermediates on the ribosome. Mol Cell 25:505-517
Munro JB, Altman RB, Tung CS, Cate JH, Sanbonmatsu KY, Blanchard SC (2010a) Spontaneous
formation of the unlocked state of the ribosome is a multistep process. Proc Natl Acad Sci USA
107:709-714
Munro JB, Altman RB, Tung CS, Sanbonmatsu KY, Blanchard SC (2010b) A fast dynamic mode
of the EF-G-bound ribosome. EMBO J 29:770-781
Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN (2010) SMOG@ctbp: simplified deploy-
ment of structure-based models in GROMACS. Nucleic Acids Res 38(Suppl):W657-W661
Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V (2001)
Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897-902
Pioletti M, Schlunzen F, Harms J, Zarivach R, Gluhmann M, Avila H, Bashan A, Bartels H, Auerbach
T, Jacobi C, Hartsch T, Yonath A, Franceschi F (2001) Crystal structures of complexes of the
small ribosomal subunit with tetracycline; edeine and IF3. EMBO J 20:1829-1839
Ratje R et al (2010) Head swivel on the ribosome facillitates translocation via intra-subunit tRNA
hybrid sites. Nature 468:713-716
Razga F, Spackova N, Reblova K, Koca J, Leontis NB, Sponer J (2004) Ribosomal RNA kink-turn
motif-a flexible molecular hinge. J Biomol Struct Dyn 22:183-194
Razga F, Koca J, Sponer J, Leontis NB (2005) Hinge-like motions in RNA kink-turns: the role of
the second a-minor motif and nominally unpaired bases. Biophys J 88:3466-3485
Sanbonmatsu KY (2006) Energy landscape of the ribosomal decoding center. Biochimie
88:1053-1059
Sanbonmatsu KY, Garcia AE (2002) Structure of Met-enkephalin in explicit aqueous solution
using replica exchange molecular dynamics. Proteins 46:225-234
Sanbonmatsu KY, Joseph S (2003) Understanding discrimination by the ribosome: stability testing
and groove measurement of codon-anticodon pairs. J Mol Biol 328:33-47
Sanbonmatsu KY, Joseph S, Tung CS (2005) Simulating movement of tRNA into the ribosome
during decoding. Proc Natl Acad Sci USA 102:15854-15859
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H,
Agmon I, Franceschi F, Yonath A (2000) Structure of functionally activated small ribosomal
subunit at 3.3 angstrom resolution. Cell 102:615-623
Schlunzen F, Zarivach R, Harms R, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F (2001)
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubac-
teria. Nature 413:814-821
Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005)
Structures of the bacterial ribosome at 3.5 A resolution. Science 310:827-834
Selmer M, Dunham CM, Murphy FVt, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan
V (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science
313:1935-1942
Shoemaker BA, Portman JJ, Wolynes PG (2000) Speeding molecular recognition by using the
folding funnel: the fly-casting mechanism. Proc Natl Acad Sci USA 97:8868-8873
Sporlein S, Carstens H, Satzger H, Renner C, Behrendt R, Moroder L, Tavan P, Zinth W, Wachtveitl
J (2002) Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and
validates molecular dynamics simulation. Proc Natl Acad Sci USA 99:7998-8002
Tama F, Valle M, Frank J, Brooks CL 3rd (2003) Dynamic reorganization of the functionally active
ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci
USA 100:9319-9323
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