메뉴 건너뛰기




Volumn 9, Issue 1, 2012, Pages

Rapid simulation of protein motion: Merging flexibility, rigidity and normal mode analyses

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84856954623     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/9/1/016008     Document Type: Article
Times cited : (32)

References (41)
  • 1
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • DOI 10.1038/nature06522, PII NATURE06522
    • Henzler-Wildman K and Kern D 2007 Dynamic personalities of proteins Nature 450 964-72 (Pubitemid 350273626)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 2
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • Shaw D E et al 2010 Atomic-level characterization of the structural dynamics of proteins Science 330 341-6
    • (2010) Science , vol.330 , pp. 341-346
    • Shaw, D.E.1
  • 3
    • 33645798851 scopus 로고    scopus 로고
    • The fluorescent toolbox for assessing protein location and function
    • Giepmans B N G, Adams S R, Ellison M H and Tsien R Y 2006 The fluorescent toolbox for assessing protein location and function Science 312 217-24
    • (2006) Science , vol.312 , pp. 217-224
    • Giepmans, B.N.G.1    Adams, S.R.2    Ellison, M.H.3    Tsien, R.Y.4
  • 5
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: Toy models or predictive tools?
    • Clementi C 2008 Coarse-grained models of protein folding: toy models or predictive tools? Curr. Opin. Struct. Biol. 18 10-5
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , Issue.1 , pp. 10-15
    • Clementi, C.1
  • 6
    • 38449085599 scopus 로고    scopus 로고
    • Chemistry across scales: From molecules to cells
    • Yaliraki S N and Barahona M 2007 Chemistry across scales: from molecules to cells Phil. Trans. R. Soc. A 365 2921-34
    • (2007) Phil. Trans. R. Soc. , vol.365 , pp. 2921-2934
    • Yaliraki, S.N.1    Barahona, M.2
  • 9
    • 70350714701 scopus 로고    scopus 로고
    • Comparative analysis of rigidity across protein families
    • Wells S A, Jimenez-Roldan J E and Römer R A 2009 Comparative analysis of rigidity across protein families Phys. Biol. 6 046005
    • (2009) Phys. Biol. , vol.6 , Issue.4 , pp. 046005
    • Wells, S.A.1    Jimenez-Roldan, J.E.2    Römer, R.A.3
  • 10
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • Wells S A, Menor S, Hespenheide B M and Thorpe M F 2005 Constrained geometric simulation of diffusive motion in proteins Phys. Biol. 2 S127-36
    • (2005) Phys. Biol. , vol.2 , Issue.4
    • Wells, S.A.1    Menor, S.2    Hespenheide, B.M.3    Thorpe, M.F.4
  • 12
    • 41449099769 scopus 로고    scopus 로고
    • Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
    • Jolley C C, Wells S A, Fromme P and Thorpe M F 2008 Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations Biophys. J. 94 1613-21
    • (2008) Biophys. J. , vol.94 , pp. 1613-1621
    • Jolley, C.C.1    Wells, S.A.2    Fromme, P.3    Thorpe, M.F.4
  • 13
    • 3242875210 scopus 로고    scopus 로고
    • ElNémo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre K and Sanejouand Y-H 2004 ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucl. Acids Res. 32 610-4
    • (2004) Nucl. Acids Res. , vol.32 , Issue.WEB SERVER , pp. 610-614
    • Suhre, K.1    Sanejouand, Y.-H.2
  • 14
  • 15
    • 77949634796 scopus 로고    scopus 로고
    • Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins
    • Bahar I, Lezon T R, Bakan A and Shrivastava I H 2010 Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem. Rev. 110 1463-97
    • (2010) Chem. Rev. , vol.110 , pp. 1463-1497
    • Bahar, I.1    Lezon, T.R.2    Bakan, A.3    Shrivastava, I.H.4
  • 16
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • DOI 10.1016/j.str.2005.02.002
    • Ma J 2005 Usefulness and limitations of normal mode analysis in modelling dynamics of biomolecular complexes Structure 13 373-80 (Pubitemid 40342876)
    • (2005) Structure , vol.13 , Issue.3 , pp. 373-380
    • Ma, J.1
  • 17
    • 34248159870 scopus 로고    scopus 로고
    • Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics
    • DOI 10.1016/j.str.2007.03.013, PII S0969212607001414
    • Rueda M, Chacón P and Orozco M 2007 Thorough validation of protein normal mode analysis: a comparative study with essential dynamics Structure 15 565-75 (Pubitemid 46722600)
    • (2007) Structure , vol.15 , Issue.5 , pp. 565-575
    • Rueda, M.1    Chacon, P.2    Orozco, M.3
  • 19
    • 78249233614 scopus 로고    scopus 로고
    • Normal mode analysis and applications in biological physics
    • Dykeman E C and Sankey O F 2010 Normal mode analysis and applications in biological physics J. Phys.: Condens. Matter 22 423202
    • (2010) J. Phys.: Condens. Matter , vol.22 , Issue.42 , pp. 423202
    • Dykeman, E.C.1    Sankey, O.F.2
  • 21
    • 0021603710 scopus 로고
    • Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II
    • DOI 10.1016/S0022-2836(84)80006-6
    • Wlodawer A, Walter J, Huber R and Sjolin L 1984 Structure of bovine pancreatic trypsin inhibitor: results of joint neutron and X-ray refinement of crystal form II J. Mol. Biol. 180 301-29 (Pubitemid 15050101)
    • (1984) Journal of Molecular Biology , vol.180 , Issue.2 , pp. 301-329
    • Wlodawer, A.1    Walter, J.2    Huber, R.3    Sjolin, L.4
  • 22
    • 0024235168 scopus 로고
    • Reduced bovine pancreatic trypsin inhibitor has a compact structure
    • DOI 10.1021/bi00425a003
    • Amir D and Haas E 1988 Reduced bovine pancreatic trypsin inhibitor has a compact structure Biochemistry 27 8889-93 (Pubitemid 19021271)
    • (1988) Biochemistry , vol.27 , Issue.25 , pp. 8889-8893
    • Amir, D.1    Haas, E.2
  • 24
    • 0343193210 scopus 로고    scopus 로고
    • 1-antitrypsin reveals targets for rational drug design to prevent conformational disease
    • Elliott P R, Pei X Y, Dafforn T R and Lomas D A 2000 Topography of a 2.0 structure of α-1-antitrypsin reveals targets for rational drug design to prevent conformational disease Protein Sci. 9 1274-81 (Pubitemid 30602280)
    • (2000) Protein Science , vol.9 , Issue.7 , pp. 1274-1281
    • Elliott, P.R.1    Pie, X.Y.2    Dafforn, T.R.3    Lomas, D.A.4
  • 25
    • 0036198797 scopus 로고    scopus 로고
    • Protein disulfide isomerases exploit synergy between catalytic and specific binding domains
    • DOI 10.1093/embo-reports/kvf035
    • Freedman R B, Klappa P and Ruddock L W 2002 Protein disulfide isomerases exploit synergy between catalytic and specific binding domains EMBO Rep. 15 136-40 (Pubitemid 34213490)
    • (2002) EMBO Reports , vol.3 , Issue.2 , pp. 136-140
    • Freedman, R.B.1    Klappa, P.2    Ruddock, L.W.3
  • 26
    • 57749102824 scopus 로고    scopus 로고
    • The catalytic activity of protein-disulfide isomerase requires a conformationally flexible molecule
    • Tian G, Kober F, Lewandrowski U, Sickmann A, Lennarz W J and Schindelin H 2008 The catalytic activity of protein-disulfide isomerase requires a conformationally flexible molecule J. Biol. Chem. 283 33630-40
    • (2008) J. Biol. Chem. , vol.283 , pp. 33630-33640
    • Tian, G.1    Kober, F.2    Lewandrowski, U.3    Sickmann, A.4    Lennarz, W.J.5    Schindelin, H.6
  • 27
    • 30344444015 scopus 로고    scopus 로고
    • The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites
    • DOI 10.1016/j.cell.2005.10.044, PII S0092867405014121
    • Tian G, Xiang S, Noiva R, Lennarz W J and Schindelin H 2006 The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites Cell 124 61-73 (Pubitemid 43069310)
    • (2006) Cell , vol.124 , Issue.1 , pp. 61-73
    • Tian, G.1    Xiang, S.2    Noiva, R.3    Lennarz, W.J.4    Schindelin, H.5
  • 28
    • 41149168686 scopus 로고    scopus 로고
    • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    • DOI 10.1038/nature06717, PII NATURE06717
    • Hilf R J C and Dutzler R 2008 X-ray structure of a prokaryotic pentameric ligand-gated ion channel Nature 452 375-9 (Pubitemid 351430790)
    • (2008) Nature , vol.452 , Issue.7185 , pp. 375-379
    • Hilf, R.J.C.1    Dutzler, R.2
  • 29
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • DOI 10.1006/jmbi.1998.2401
    • Word J M, Lovell S C, Richardson J S and Richardsonzhed D C 1999 Asparagine and glutamine: using hydrogen atoms contacts in the choice of side chain amide orientation J. Mol. Biol. 285 1735-47 (Pubitemid 29060467)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.4 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 31
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M M 1996 Large amplitude elastic motions in proteins from single-parameter atomic analysis Phys. Rev. Lett. 77 1905-8 (Pubitemid 126625816)
    • (1996) Physical Review Letters , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.M.1
  • 33
    • 28844448877 scopus 로고    scopus 로고
    • Channel opening motion of α7 nicotinic acetylcholine receptor as suggested by normal mode analysis
    • DOI 10.1016/j.jmb.2005.10.039, PII S0022283605012830
    • Cheng X, Lu B, Grant B, Law R J and McCammon J A 2006 Channel opening motion of α7 nicotinic acetylcholine receptor as suggested by normal mode analysis J. Mol. Biol. 355 310-24 (Pubitemid 41774133)
    • (2006) Journal of Molecular Biology , vol.355 , Issue.2 , pp. 310-324
    • Cheng, X.1    Lu, B.2    Grant, B.3    Law, R.J.4    McCammon, J.A.5
  • 34
    • 0141792364 scopus 로고    scopus 로고
    • Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T-R2 transition
    • DOI 10.1016/j.jmb.2003.08.027
    • Xy C, Tobi D and Bahar I 2003 Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T-R2 transition J. Mol. Biol. 333 153-68 (Pubitemid 37153272)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.1 , pp. 153-168
    • Xu, C.1    Tobi, D.2    Bahar, I.3
  • 36
    • 77957948190 scopus 로고    scopus 로고
    • Generating stereochemically-acceptable protein pathways
    • Farrell D W, Speranskiy K and Thorpe M F 2010 Generating stereochemically-acceptable protein pathways Proteins 78 2908-21
    • (2010) Proteins , vol.78 , pp. 2908-2921
    • Farrell, D.W.1    Speranskiy, K.2    Thorpe, M.F.3
  • 37
    • 79955901922 scopus 로고    scopus 로고
    • Integration of FIRST, FRODA and NMM in a coarse grained method to study protein disulphide isomerase conformational change
    • Jimenez-Roldan J E, Wells S A, Freedman R B and Roemer R A 2011 Integration of FIRST, FRODA and NMM in a coarse grained method to study protein disulphide isomerase conformational change J. Phys.: Conf. Ser. 286 012002
    • (2011) J. Phys.: Conf. Ser. , vol.286 , Issue.1 , pp. 012002
    • Jimenez-Roldan, J.E.1    Wells, S.A.2    Freedman, R.B.3    Roemer, R.A.4
  • 38
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • DOI 10.1002/prot.10168
    • Krebs W G, Alexandrov V, Wilson C A, Echols E, Yu H and Gerstein M 2002 Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins 48 682-95 (Pubitemid 34925457)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.4 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 40
    • 84856960506 scopus 로고    scopus 로고
    • Belfield W, Cole D and Payne M in preparation
    • Belfield W, Cole D and Payne M in preparation
  • 41
    • 84856960505 scopus 로고    scopus 로고
    • Exploring the energy landscapes of protein folding simulations with Bayesian computation
    • Burkoff N S, Varnai C, Wells S A and Wild D L 2011 Exploring the energy landscapes of protein folding simulations with Bayesian computation Proc. Natl Acad. Sci. at press (arXiv:1010.4735)
    • (2011) Proc. Natl Acad. Sci.
    • Burkoff, N.S.1    Varnai, C.2    Wells, S.A.3    Wild, D.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.