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Volumn 8, Issue 5, 2012, Pages

A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; MOLECULAR DYNAMICS; RNA;

EID: 84863666750     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002530     Document Type: Article
Times cited : (22)

References (75)
  • 1
    • 0033229970 scopus 로고    scopus 로고
    • The economics of ribosome biosynthesis in yeast
    • Warner JR, (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24: 437-440.
    • (1999) Trends Biochem Sci , vol.24 , pp. 437-440
    • Warner, J.R.1
  • 2
    • 34250377197 scopus 로고    scopus 로고
    • The weird and wonderful world of bacterial ribosome regulation
    • Wilson DN, Nierhaus KH, (2007) The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42: 187-219.
    • (2007) Crit Rev Biochem Mol Biol , vol.42 , pp. 187-219
    • Wilson, D.N.1    Nierhaus, K.H.2
  • 3
    • 0014693477 scopus 로고
    • Structure and Function of Escherichia Coli Ribosomes. 6. Mechanism of Assembly of 30-S Ribosomes Studied in Vitro
    • Traub P, Nomura M, (1969) Structure and Function of Escherichia Coli Ribosomes. 6. Mechanism of Assembly of 30-S Ribosomes Studied in Vitro. J Mol Biol 40: 391-&.
    • (1969) J Mol Biol , vol.40 , pp. 391
    • Traub, P.1    Nomura, M.2
  • 4
    • 0014266752 scopus 로고
    • Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins
    • Traub P, Nomura M, (1968) Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins. Proc Natl Acad Sci U S A 59: 777-784.
    • (1968) Proc Natl Acad Sci U S A , vol.59 , pp. 777-784
    • Traub, P.1    Nomura, M.2
  • 5
    • 0014432916 scopus 로고
    • Structure and function of Escherichia coli ribosomes. 3. Stoichiometry and rate of the reconstitution of ribosomes from subribosomal particles and split proteins
    • Nomura M, Traub P, (1968) Structure and function of Escherichia coli ribosomes. 3. Stoichiometry and rate of the reconstitution of ribosomes from subribosomal particles and split proteins. J Mol Biol 34: 609-619.
    • (1968) J Mol Biol , vol.34 , pp. 609-619
    • Nomura, M.1    Traub, P.2
  • 6
    • 0037319895 scopus 로고    scopus 로고
    • Assembly of the 30S ribosomal subunit
    • Culver GM, (2003) Assembly of the 30S ribosomal subunit. Biopolymers 68: 234-249.
    • (2003) Biopolymers , vol.68 , pp. 234-249
    • Culver, G.M.1
  • 7
    • 0016153699 scopus 로고
    • Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies
    • Held WA, Ballou B, Mizushima S, Nomura M, (1974) Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem 249: 3103-3111.
    • (1974) J Biol Chem , vol.249 , pp. 3103-3111
    • Held, W.A.1    Ballou, B.2    Mizushima, S.3    Nomura, M.4
  • 8
    • 0027171312 scopus 로고
    • Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits
    • Powers T, Daubresse G, Noller HF, (1993) Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits. J Mol Biol 232: 362-374.
    • (1993) J Mol Biol , vol.232 , pp. 362-374
    • Powers, T.1    Daubresse, G.2    Noller, H.F.3
  • 11
    • 0032549780 scopus 로고    scopus 로고
    • RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
    • Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA, (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279: 1940-1943.
    • (1998) Science , vol.279 , pp. 1940-1943
    • Sclavi, B.1    Sullivan, M.2    Chance, M.R.3    Brenowitz, M.4    Woodson, S.A.5
  • 12
    • 22544466402 scopus 로고    scopus 로고
    • Protein-independent folding pathway of the 16S rRNA 5′ domain
    • Adilakshmi T, Ramaswamy P, Woodson SA, (2005) Protein-independent folding pathway of the 16S rRNA 5′ domain. J Mol Biol 351: 508-519.
    • (2005) J Mol Biol , vol.351 , pp. 508-519
    • Adilakshmi, T.1    Ramaswamy, P.2    Woodson, S.A.3
  • 13
    • 0029286628 scopus 로고
    • Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA
    • Powers T, Noller HF, (1995) Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1: 194-209.
    • (1995) RNA , vol.1 , pp. 194-209
    • Powers, T.1    Noller, H.F.2
  • 14
    • 38049055218 scopus 로고    scopus 로고
    • Assembly of the 5′ and 3′ minor domains of 16S ribosomal RNA as monitored by tethered probing from ribosomal protein S20
    • Dutca LM, Culver GM, (2008) Assembly of the 5′ and 3′ minor domains of 16S ribosomal RNA as monitored by tethered probing from ribosomal protein S20. J Mol Biol 376: 92-108.
    • (2008) J Mol Biol , vol.376 , pp. 92-108
    • Dutca, L.M.1    Culver, G.M.2
  • 15
    • 0033655152 scopus 로고    scopus 로고
    • Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes
    • Culver GM, Noller HF, (2000) Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes. Methods Enzymol 318: 461-475.
    • (2000) Methods Enzymol , vol.318 , pp. 461-475
    • Culver, G.M.1    Noller, H.F.2
  • 16
    • 28444479853 scopus 로고    scopus 로고
    • An assembly landscape for the 30S ribosomal subunit
    • Talkington MW, Siuzdak G, Williamson JR, (2005) An assembly landscape for the 30S ribosomal subunit. Nature 438: 628-632.
    • (2005) Nature , vol.438 , pp. 628-632
    • Talkington, M.W.1    Siuzdak, G.2    Williamson, J.R.3
  • 17
    • 55249084867 scopus 로고    scopus 로고
    • Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly
    • Adilakshmi T, Bellur DL, Woodson SA, (2008) Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature 455: 1268-1272.
    • (2008) Nature , vol.455 , pp. 1268-1272
    • Adilakshmi, T.1    Bellur, D.L.2    Woodson, S.A.3
  • 19
    • 27644502679 scopus 로고    scopus 로고
    • Simulating movement of tRNA into the ribosome during decoding
    • Sanbonmatsu KY, Joseph S, Tung CS, (2005) Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 102: 15854-15859.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15854-15859
    • Sanbonmatsu, K.Y.1    Joseph, S.2    Tung, C.S.3
  • 20
    • 77952717308 scopus 로고    scopus 로고
    • Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
    • Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, et al. (2010) Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16: 1196-1204.
    • (2010) RNA , vol.16 , pp. 1196-1204
    • Whitford, P.C.1    Geggier, P.2    Altman, R.B.3    Blanchard, S.C.4    Onuchic, J.N.5
  • 21
    • 77957159348 scopus 로고    scopus 로고
    • Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome
    • Whitford PC, Onuchic JN, Sanbonmatsu KY, (2010) Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc 132: 13170-13171.
    • (2010) J Am Chem Soc , vol.132 , pp. 13170-13171
    • Whitford, P.C.1    Onuchic, J.N.2    Sanbonmatsu, K.Y.3
  • 22
    • 77956935085 scopus 로고    scopus 로고
    • The role of L1 stalk-tRNA interaction in the ribosome elongation cycle
    • Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, et al. (2010) The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol 402: 741-760.
    • (2010) J Mol Biol , vol.402 , pp. 741-760
    • Trabuco, L.G.1    Schreiner, E.2    Eargle, J.3    Cornish, P.4    Ha, T.5
  • 23
    • 0037453255 scopus 로고    scopus 로고
    • Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs
    • 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.
    • (2003) J Mol Biol , vol.328 , pp. 33-47
    • Sanbonmatsu, K.Y.1    Joseph, S.2
  • 24
    • 33846039881 scopus 로고    scopus 로고
    • Energetics of codon-anticodon recognition on the small ribosomal subunit
    • Almlof M, Ander M, Aqvist J, (2007) Energetics of codon-anticodon recognition on the small ribosomal subunit. Biochemistry 46: 200-209.
    • (2007) Biochemistry , vol.46 , pp. 200-209
    • Almlof, M.1    Ander, M.2    Aqvist, J.3
  • 25
    • 58149310718 scopus 로고    scopus 로고
    • The ribosome structure controls and directs mRNA entry, translocation and exit dynamics
    • Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL, (2008) The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Phys Biol 5: 046005.
    • (2008) Phys Biol , vol.5 , pp. 046005
    • Kurkcuoglu, O.1    Doruker, P.2    Sen, T.Z.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 26
    • 77952589053 scopus 로고    scopus 로고
    • Recognition of the regulatory nascent chain TnaC by the ribosome
    • Trabuco LG, Harrison CB, Schreiner E, Schulten K, (2010) Recognition of the regulatory nascent chain TnaC by the ribosome. Structure 18: 627-637.
    • (2010) Structure , vol.18 , pp. 627-637
    • Trabuco, L.G.1    Harrison, C.B.2    Schreiner, E.3    Schulten, K.4
  • 27
  • 28
    • 33747873906 scopus 로고    scopus 로고
    • Energy landscape of the ribosomal decoding center
    • Sanbonmatsu KY, (2006) Energy landscape of the ribosomal decoding center. Biochimie 88: 1053-1059.
    • (2006) Biochimie , vol.88 , pp. 1053-1059
    • Sanbonmatsu, K.Y.1
  • 29
    • 33747880625 scopus 로고    scopus 로고
    • A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns
    • Vaiana AC, Westhof E, Auffinger P, (2006) A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns. Biochimie 88: 1061-1073.
    • (2006) Biochimie , vol.88 , pp. 1061-1073
    • Vaiana, A.C.1    Westhof, E.2    Auffinger, P.3
  • 30
    • 57449090256 scopus 로고    scopus 로고
    • Molecular dynamics study of the ribosomal A-site
    • Romanowska J, Setny P, Trylska J, (2008) Molecular dynamics study of the ribosomal A-site. J Phys Chem B 112: 15227-15243.
    • (2008) J Phys Chem B , vol.112 , pp. 15227-15243
    • Romanowska, J.1    Setny, P.2    Trylska, J.3
  • 31
    • 59849110790 scopus 로고    scopus 로고
    • Stochastic gating and drug-ribosome interactions
    • Vaiana AC, Sanbonmatsu KY, (2009) Stochastic gating and drug-ribosome interactions. J Mol Biol 386: 648-661.
    • (2009) J Mol Biol , vol.386 , pp. 648-661
    • Vaiana, A.C.1    Sanbonmatsu, K.Y.2
  • 32
    • 78649888301 scopus 로고    scopus 로고
    • A combined molecular dynamics and rapid kinetics approach to identify conserved three-dimensional communication networks in elongation factor Tu
    • Wieden HJ, Mercier E, Gray J, Steed B, Yawney D, (2010) A combined molecular dynamics and rapid kinetics approach to identify conserved three-dimensional communication networks in elongation factor Tu. Biophys J 99: 3735-3743.
    • (2010) Biophys J , vol.99 , pp. 3735-3743
    • Wieden, H.J.1    Mercier, E.2    Gray, J.3    Steed, B.4    Yawney, D.5
  • 33
    • 79959935915 scopus 로고    scopus 로고
    • Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome
    • Adamczyk AJ, Warshel A, (2011) Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proc Natl Acad Sci U S A 108: 9827-9832.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 9827-9832
    • Adamczyk, A.J.1    Warshel, A.2
  • 34
    • 24644461086 scopus 로고    scopus 로고
    • Mechanism of peptide bond synthesis on the ribosome
    • Trobro S, Aqvist J, (2005) Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A 102: 12395-12400.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 12395-12400
    • Trobro, S.1    Aqvist, J.2
  • 35
    • 23944472625 scopus 로고    scopus 로고
    • What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?
    • Sharma PK, Xiang Y, Kato M, Warshel A, (2005) What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry 44: 11307-11314.
    • (2005) Biochemistry , vol.44 , pp. 11307-11314
    • Sharma, P.K.1    Xiang, Y.2    Kato, M.3    Warshel, A.4
  • 36
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson JR, (2000) Induced fit in RNA-protein recognition. Nat Struct Biol 7: 834-837.
    • (2000) Nat Struct Biol , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 37
    • 0032102374 scopus 로고    scopus 로고
    • Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome
    • Ramakrishnan V, White SW, (1998) Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends Biochem Sci 23: 208-212.
    • (1998) Trends Biochem Sci , vol.23 , pp. 208-212
    • Ramakrishnan, V.1    White, S.W.2
  • 38
    • 0037453294 scopus 로고    scopus 로고
    • A structural model for the assembly of the 30S subunit of the ribosome
    • Stagg SM, Mears JA, Harvey SC, (2003) A structural model for the assembly of the 30S subunit of the ribosome. J Mol Biol 328: 49-61.
    • (2003) J Mol Biol , vol.328 , pp. 49-61
    • Stagg, S.M.1    Mears, J.A.2    Harvey, S.C.3
  • 39
    • 23744516552 scopus 로고    scopus 로고
    • Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach
    • Trylska J, McCammon JA, Brooks CL Iii, (2005) Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc 127: 11125-11133.
    • (2005) J Am Chem Soc , vol.127 , pp. 11125-11133
    • Trylska, J.1    McCammon, J.A.2    Brooks Iii., C.L.3
  • 40
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Wang Y, Rader AJ, Bahar I, Jernigan RL, (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147: 302-314.
    • (2004) J Struct Biol , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 41
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • Trylska J, Tozzini V, McCammon JA, (2005) Exploring global motions and correlations in the ribosome. Biophys J 89: 1455-1463.
    • (2005) Biophys J , vol.89 , pp. 1455-1463
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 42
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • 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 U S A 100: 9319-9323.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks 3rd, C.L.4
  • 43
    • 66149167201 scopus 로고    scopus 로고
    • Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
    • Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL, (2009) Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 75: 837-845.
    • (2009) Proteins , vol.75 , pp. 837-845
    • Kurkcuoglu, O.1    Kurkcuoglu, Z.2    Doruker, P.3    Jernigan, R.L.4
  • 44
  • 45
    • 58149157892 scopus 로고    scopus 로고
    • Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome
    • Yan A, Wang Y, Kloczkowski A, Jernigan RL, (2008) Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. J Chem Theory Comput 4: 1757-1767.
    • (2008) J Chem Theory Comput , vol.4 , pp. 1757-1767
    • Yan, A.1    Wang, Y.2    Kloczkowski, A.3    Jernigan, R.L.4
  • 46
    • 2942615089 scopus 로고    scopus 로고
    • The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
    • Klein DJ, Moore PB, Steitz TA, (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol 340: 141-177.
    • (2004) J Mol Biol , vol.340 , pp. 141-177
    • Klein, D.J.1    Moore, P.B.2    Steitz, T.A.3
  • 48
    • 0034615759 scopus 로고    scopus 로고
    • Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain
    • Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR, (2000) Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science 288: 107-113.
    • (2000) Science , vol.288 , pp. 107-113
    • Agalarov, S.C.1    Sridhar Prasad, G.2    Funke, P.M.3    Stout, C.D.4    Williamson, J.R.5
  • 49
    • 0035850733 scopus 로고    scopus 로고
    • Central domain assembly: Thermodynamics and kinetics of S6 and S18 binding to an S15-RNA complex
    • Recht MI, Williamson JR, (2001) Central domain assembly: Thermodynamics and kinetics of S6 and S18 binding to an S15-RNA complex. J Mol Biol 313: 35-48.
    • (2001) J Mol Biol , vol.313 , pp. 35-48
    • Recht, M.I.1    Williamson, J.R.2
  • 50
    • 0042063940 scopus 로고    scopus 로고
    • Affinity of ribosomal protein S8 from mesophilic and (hyper)thermophilic archaea and bacteria for 16S rRNA correlates with the growth temperatures of the organisms
    • Gruber T, Kohrer C, Lung B, Shcherbakov D, Piendl W, (2003) Affinity of ribosomal protein S8 from mesophilic and (hyper)thermophilic archaea and bacteria for 16S rRNA correlates with the growth temperatures of the organisms. FEBS Lett 549: 123-128.
    • (2003) FEBS Lett , vol.549 , pp. 123-128
    • Gruber, T.1    Kohrer, C.2    Lung, B.3    Shcherbakov, D.4    Piendl, W.5
  • 52
    • 13144276305 scopus 로고    scopus 로고
    • Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
    • Clemons WM Jr, Davies C, White SW, Ramakrishnan V, (1998) Conformational variability of the N-terminal helix in the structure of ribosomal protein S15. Structure 6: 429-438.
    • (1998) Structure , vol.6 , pp. 429-438
    • Clemons Jr., W.M.1    Davies, C.2    White, S.W.3    Ramakrishnan, V.4
  • 55
    • 0031026421 scopus 로고    scopus 로고
    • Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus
    • Berglund H, Rak A, Serganov A, Garber M, Hard T, (1997) Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus. Nat Struct Biol 4: 20-23.
    • (1997) Nat Struct Biol , vol.4 , pp. 20-23
    • Berglund, H.1    Rak, A.2    Serganov, A.3    Garber, M.4    Hard, T.5
  • 56
    • 34147180422 scopus 로고    scopus 로고
    • The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA
    • Crety T, Malliavin TE, (2007) The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA. Biophys J 92: 2647-2665.
    • (2007) Biophys J , vol.92 , pp. 2647-2665
    • Crety, T.1    Malliavin, T.E.2
  • 57
    • 85047694092 scopus 로고    scopus 로고
    • Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA
    • Revtovich SV, Nikulin AD, Nikonov SV, (2004) Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA. Biochemistry (Mosc) 69: 1319-1323.
    • (2004) Biochemistry (Mosc) , vol.69 , pp. 1319-1323
    • Revtovich, S.V.1    Nikulin, A.D.2    Nikonov, S.V.3
  • 58
    • 0032849011 scopus 로고    scopus 로고
    • Identification of an RNA-protein bridge spanning the ribosomal subunit interface
    • Culver GM, Cate JH, Yusupova GZ, Yusupov MM, Noller HF, (1999) Identification of an RNA-protein bridge spanning the ribosomal subunit interface. Science 285: 2133-2136.
    • (1999) Science , vol.285 , pp. 2133-2136
    • Culver, G.M.1    Cate, J.H.2    Yusupova, G.Z.3    Yusupov, M.M.4    Noller, H.F.5
  • 59
    • 0027141109 scopus 로고
    • Ribosomal protein S17: characterization of the three-dimensional structure by 1H and 15N NMR
    • Golden BL, Hoffman DW, Ramakrishnan V, White SW, (1993) Ribosomal protein S17: characterization of the three-dimensional structure by 1H and 15N NMR. Biochemistry 32: 12812-12820.
    • (1993) Biochemistry , vol.32 , pp. 12812-12820
    • Golden, B.L.1    Hoffman, D.W.2    Ramakrishnan, V.3    White, S.W.4
  • 60
    • 0020665124 scopus 로고
    • Structural and functional studies on protein S20 from the 30-S subunit of the Escherichia coli ribosome
    • Paterakis K, Littlechild J, Woolley P, (1983) Structural and functional studies on protein S20 from the 30-S subunit of the Escherichia coli ribosome. Eur J Biochem 129: 543-548.
    • (1983) Eur J Biochem , vol.129 , pp. 543-548
    • Paterakis, K.1    Littlechild, J.2    Woolley, P.3
  • 61
    • 84863662178 scopus 로고    scopus 로고
    • Comparison of tRNA's motions in the free and ribosomal bound structures with elastic network models
    • Wang YM, Jernigan RL, (2005) Comparison of tRNA's motions in the free and ribosomal bound structures with elastic network models. Biophys J 88: 183a-183a.
    • (2005) Biophys J , vol.88
    • Wang, Y.M.1    Jernigan, R.L.2
  • 62
    • 79959582444 scopus 로고    scopus 로고
    • MAVENs: motion analysis and visualization of elastic networks and structural ensembles
    • Zimmermann MT, Kloczkowski A, Jernigan RL, (2011) MAVENs: motion analysis and visualization of elastic networks and structural ensembles. BMC Bioinformatics 12: 264.
    • (2011) BMC Bioinformatics , vol.12 , pp. 264
    • Zimmermann, M.T.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 63
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505-515.
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5
  • 66
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
    • Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE 3rd, et al. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92: 3817-3829.
    • (2007) Biophys J , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham 3rd, T.E.5
  • 68
    • 33646940952 scopus 로고
    • Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical-Integration of Cartesian Equations of Motion of a System with Constraints- Molecular-Dynamics of N-Alkanes. J Comput Phys 23: 327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 69
    • 84986440341 scopus 로고
    • Settle - an Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models
    • Miyamoto S, Kollman PA, (1992) Settle- an Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models. J Comput Chem 13: 952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 70
    • 33846823909 scopus 로고
    • Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems
    • Darden T, York D, Pedersen L, (1993) Particle Mesh Ewald- an N.Log(N) Method for Ewald Sums in Large Systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 72
    • 0000197372 scopus 로고    scopus 로고
    • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
    • Tirion MM, (1996) Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Phys Rev Lett 77: 1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 73
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B, (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2: 173-181.
    • (1997) Fold Des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 75
    • 33748469301 scopus 로고    scopus 로고
    • A new method for coarse-grained elastic normal-mode analysis
    • Ma JP, Lu MY, Poon B, (2006) A new method for coarse-grained elastic normal-mode analysis. J Chem Theory Comput 2: 464-471.
    • (2006) J Chem Theory Comput , vol.2 , pp. 464-471
    • Ma, J.P.1    Lu, M.Y.2    Poon, B.3


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