메뉴 건너뛰기




Volumn 83, Issue 12, 2015, Pages 2137-2146

Shortening a loop can increase protein native state entropy

Author keywords

Coarse grained model; Conformational entropy; Molecular dynamics; Native state dynamics; Protein folding

Indexed keywords

ACYLPHOSPHATASE; MUTANT PROTEIN; PROTEIN; PROTEIN UBC7; SOLVENT; UNCLASSIFIED DRUG; ACID ANHYDRIDE HYDROLASE; SACCHAROMYCES CEREVISIAE PROTEIN; SPECTRIN; UBC7 PROTEIN, S CEREVISIAE; UBIQUITIN CONJUGATING ENZYME;

EID: 84954383307     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24926     Document Type: Article
Times cited : (28)

References (36)
  • 1
    • 0033600802 scopus 로고    scopus 로고
    • Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery
    • Streaker ED, Beckett D. Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery. J Mol Biol 1999;292:619-632.
    • (1999) J Mol Biol , vol.292 , pp. 619-632
    • Streaker, E.D.1    Beckett, D.2
  • 2
    • 0037227422 scopus 로고    scopus 로고
    • Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen
    • Collis AVJ, Brouwer AP, Martin ACR. Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J Mol Biol 2003;325:337-354.
    • (2003) J Mol Biol , vol.325 , pp. 337-354
    • Collis, A.V.J.1    Brouwer, A.P.2    Martin, A.C.R.3
  • 6
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 2009;6:551-552.
    • (2009) Nat Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 7
    • 0030623398 scopus 로고    scopus 로고
    • An inverse correlation between loop length and stability in a four-helix-bundle protein
    • Nagi AD, Regan L. An inverse correlation between loop length and stability in a four-helix-bundle protein. Fold Des 1997;2:67-75.
    • (1997) Fold Des , vol.2 , pp. 67-75
    • Nagi, A.D.1    Regan, L.2
  • 8
    • 0030663205 scopus 로고    scopus 로고
    • Loop length, intramolecular diffusion and protein folding
    • Viguera AR, Serrano L. Loop length, intramolecular diffusion and protein folding. Nat Struct Biol 1997;4:939-946.
    • (1997) Nat Struct Biol , vol.4 , pp. 939-946
    • Viguera, A.R.1    Serrano, L.2
  • 9
    • 0031576337 scopus 로고    scopus 로고
    • Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates
    • Ladurner AG, Fersht AR. Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J Mol Biol 1997;273:330-337.
    • (1997) J Mol Biol , vol.273 , pp. 330-337
    • Ladurner, A.G.1    Fersht, A.R.2
  • 10
    • 0037305938 scopus 로고    scopus 로고
    • Low free energy cost of very long loop insertions in proteins
    • Scalley-Kim M, Minard P, Baker D. Low free energy cost of very long loop insertions in proteins. Protein Sci 2003;12:197-206.
    • (2003) Protein Sci , vol.12 , pp. 197-206
    • Scalley-Kim, M.1    Minard, P.2    Baker, D.3
  • 12
    • 36549094651 scopus 로고
    • Intrachain loops in polymers-effects of excluded volume
    • Chan HS, Dill KA. Intrachain loops in polymers-effects of excluded volume. J Chem Phys 1989;90:492-509.
    • (1989) J Chem Phys , vol.90 , pp. 492-509
    • Chan, H.S.1    Dill, K.A.2
  • 14
    • 1242338901 scopus 로고    scopus 로고
    • Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins
    • Zhou HX. Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins. Accounts Chem Res 2004;37:123-130.
    • (2004) Accounts Chem Res , vol.37 , pp. 123-130
    • Zhou, H.X.1
  • 16
    • 84873526287 scopus 로고    scopus 로고
    • The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
    • Wand AJ. The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation. Curr Opin Struc Biol 2013;23:75-81.
    • (2013) Curr Opin Struc Biol , vol.23 , pp. 75-81
    • Wand, A.J.1
  • 18
    • 80052114107 scopus 로고    scopus 로고
    • Protein dynamics whispering within
    • Bruschweiler R. Protein dynamics whispering within. Nat Chem 2011;3:665-666.
    • (2011) Nat Chem , vol.3 , pp. 665-666
    • Bruschweiler, R.1
  • 19
    • 0035128571 scopus 로고    scopus 로고
    • Atomic resolution structure of a mutant of the spectrin SH3 domain
    • Berisio R, Viguera A, Serrano L, Wilmanns M. Atomic resolution structure of a mutant of the spectrin SH3 domain. Acta Crystallogr D 2001;57:337-340.
    • (2001) Acta Crystallogr D , vol.57 , pp. 337-340
    • Berisio, R.1    Viguera, A.2    Serrano, L.3    Wilmanns, M.4
  • 20
    • 0029760326 scopus 로고    scopus 로고
    • Different folding transition states may result in the same native structure
    • Viguera AR, Serrano L, Wilmanns M. Different folding transition states may result in the same native structure. Nat Struct Biol 1996;3:874-880.
    • (1996) Nat Struct Biol , vol.3 , pp. 874-880
    • Viguera, A.R.1    Serrano, L.2    Wilmanns, M.3
  • 21
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling
    • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 22
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008;4:435-447.
    • (2008) J Chem Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 25
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys 2007;126:014101
    • (2007) J Chem Phys , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 27
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001;115:6289-6292.
    • (2001) J Chem Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 28
    • 73949098933 scopus 로고    scopus 로고
    • Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties
    • Baron R, Hunenberger PH, McCammon JA. Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties. J Chem Theory Comput 2009;5:3150-3160.
    • (2009) J Chem Theory Comput , vol.5 , pp. 3150-3160
    • Baron, R.1    Hunenberger, P.H.2    McCammon, J.A.3
  • 29
    • 63749108613 scopus 로고    scopus 로고
    • In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides
    • 118108-1-118108-4
    • Li DW, Bruschweiler R. In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides. Phys Rev Lett 2009;102:118108-1-118108-4.
    • (2009) Phys Rev Lett , vol.102
    • Li, D.W.1    Bruschweiler, R.2
  • 31
    • 84866679728 scopus 로고    scopus 로고
    • Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles
    • Baxa MC, Haddadian EJ, Jha AK, Freed KF, Sosnick TR. Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles. J Am Chem Soc 2012;134:15929-15936.
    • (2012) J Am Chem Soc , vol.134 , pp. 15929-15936
    • Baxa, M.C.1    Haddadian, E.J.2    Jha, A.K.3    Freed, K.F.4    Sosnick, T.R.5
  • 32
    • 84908288276 scopus 로고    scopus 로고
    • Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
    • Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci USA 2014;111:15396-15401.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 15396-15401
    • Baxa, M.C.1    Haddadian, E.J.2    Jumper, J.M.3    Freed, K.F.4    Sosnick, T.R.5
  • 33
    • 84859571593 scopus 로고    scopus 로고
    • Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
    • Numata J, Knapp EW. Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories. J Chem Theory Comput 2012;8:1235-1245.
    • (2012) J Chem Theory Comput , vol.8 , pp. 1235-1245
    • Numata, J.1    Knapp, E.W.2
  • 34
    • 79960913321 scopus 로고    scopus 로고
    • Calculation of configurational entropy with a Boltzmann-Quasiharmonic model: the origin of high-affinity protein-ligand binding
    • Harpole KW, Sharp KA. Calculation of configurational entropy with a Boltzmann-Quasiharmonic model: the origin of high-affinity protein-ligand binding. J Phys Chem B 2011;115:9461-9472.
    • (2011) J Phys Chem B , vol.115 , pp. 9461-9472
    • Harpole, K.W.1    Sharp, K.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.