메뉴 건너뛰기




Volumn 82, Issue 4, 2014, Pages 668-678

Temperature effects on the hydrodynamic radius of the intrinsically disordered N-terminal region of the p53 protein

Author keywords

Acidic activation domain; Heat; Hydrodynamic radius; Intrinsically disordered protein; Net charge; Polyproline

Indexed keywords

GLYCINE; INTRINSICALLY DISORDERED PROTEIN; POLYPEPTIDE; PROLINE; PROTEIN P53;

EID: 84895548711     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24449     Document Type: Article
Times cited : (38)

References (59)
  • 2
    • 84862074830 scopus 로고    scopus 로고
    • Carbon-detected 15N NMR spin relaxation of an intrinsically disordered protein: FCP1 dynamics unbound and in complex with RAP74
    • Lawrence CW, Showalter SA. Carbon-detected 15N NMR spin relaxation of an intrinsically disordered protein: FCP1 dynamics unbound and in complex with RAP74. J Phys Chem Lett 2012;3:1409-1413.
    • (2012) J Phys Chem Lett , vol.3 , pp. 1409-1413
    • Lawrence, C.W.1    Showalter, S.A.2
  • 4
    • 79953838275 scopus 로고    scopus 로고
    • Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins
    • Choi UB, McCann JJ, Weninger KR, Bowen ME. Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins. Cell 2011;19:566-576.
    • (2011) Cell , vol.19 , pp. 566-576
    • Choi, U.B.1    McCann, J.J.2    Weninger, K.R.3    Bowen, M.E.4
  • 5
    • 84870057622 scopus 로고    scopus 로고
    • Intrinsically disordered proteins: a 10-year recap
    • Tompa P. Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci 2012;37:509-516.
    • (2012) Trends Biochem Sci , vol.37 , pp. 509-516
    • Tompa, P.1
  • 6
    • 60349087841 scopus 로고    scopus 로고
    • Biophysical characterization of intrinsically disordered proteins
    • Eliezer D. Biophysical characterization of intrinsically disordered proteins. Curr Opin Struct Biol 2009;19:23-30.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 23-30
    • Eliezer, D.1
  • 7
    • 71749087100 scopus 로고    scopus 로고
    • Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings
    • Nodet G, Salmon L, Ozenne V, Meier S, Jensen MR, Blackledge M. Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings. J Am Chem Soc 2009;131:17908-17918.
    • (2009) J Am Chem Soc , vol.131 , pp. 17908-17918
    • Nodet, G.1    Salmon, L.2    Ozenne, V.3    Meier, S.4    Jensen, M.R.5    Blackledge, M.6
  • 8
    • 77950403640 scopus 로고    scopus 로고
    • Defining conformational ensembles of intrinsically disordered and partially folded proteins directly from chemical shifts
    • Jensen MR, Salmon L, Nodet G, Blackledge M. Defining conformational ensembles of intrinsically disordered and partially folded proteins directly from chemical shifts. J Am Chem Soc 2010;132:1270-1272.
    • (2010) J Am Chem Soc , vol.132 , pp. 1270-1272
    • Jensen, M.R.1    Salmon, L.2    Nodet, G.3    Blackledge, M.4
  • 10
    • 27144528728 scopus 로고    scopus 로고
    • Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation
    • Sivakolundu SG, Bashford D, Kriwacki, RW. Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation. J Mol Biol 2005;353:1118-1128.
    • (2005) J Mol Biol , vol.353 , pp. 1118-1128
    • Sivakolundu, S.G.1    Bashford, D.2    Kriwacki, R.W.3
  • 11
    • 77951631601 scopus 로고    scopus 로고
    • Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase
    • Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, Tyers M, Forman-Kay JD. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 2010;18:494-506.
    • (2010) Structure , vol.18 , pp. 494-506
    • Mittag, T.1    Marsh, J.2    Grishaev, A.3    Orlicky, S.4    Lin, H.5    Sicheri, F.6    Tyers, M.7    Forman-Kay, J.D.8
  • 13
    • 77951645923 scopus 로고    scopus 로고
    • Sequence determinants of compaction in intrinsically disordered proteins
    • Marsh JA, Forman-Kay JD. Sequence determinants of compaction in intrinsically disordered proteins. Biophys J 2010;98:2383-2390.
    • (2010) Biophys J , vol.98 , pp. 2383-2390
    • Marsh, J.A.1    Forman-Kay, J.D.2
  • 14
    • 0030941458 scopus 로고    scopus 로고
    • p53, the cellular gatekeeper for growth and division
    • Levine AJ. p53, the cellular gatekeeper for growth and division. Cell 1997;88:323-331.
    • (1997) Cell , vol.88 , pp. 323-331
    • Levine, A.J.1
  • 15
    • 0032568539 scopus 로고    scopus 로고
    • Identification of an additional negative regulatory region for p53 sequence-specific DNA binding
    • Müller-Tiemann BF, Halazonetis TD, Elting JJ. Identification of an additional negative regulatory region for p53 sequence-specific DNA binding. Proc Natl Acad Sci USA 1998;95:6079-6084.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6079-6084
    • Müller-Tiemann, B.F.1    Halazonetis, T.D.2    Elting, J.J.3
  • 16
    • 77955099224 scopus 로고    scopus 로고
    • Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II
    • Kjaergaard M, Nørholm AB, Hendus-Altenburger R, Pedersen SF, Poulsen FM, Kragelund BB. Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II. Protein Sci 2010;19:1555-1564.
    • (2010) Protein Sci , vol.19 , pp. 1555-1564
    • Kjaergaard, M.1    Nørholm, A.B.2    Hendus-Altenburger, R.3    Pedersen, S.F.4    Poulsen, F.M.5    Kragelund, B.B.6
  • 17
    • 84867688574 scopus 로고    scopus 로고
    • Thermal unfolding of the N-terminal region of p53 monitored by circular dichroism spectroscopy
    • Schaub LJ, Campbell JC, Whitten ST. Thermal unfolding of the N-terminal region of p53 monitored by circular dichroism spectroscopy. Protein Sci 2012;21:1682-1688.
    • (2012) Protein Sci , vol.21 , pp. 1682-1688
    • Schaub, L.J.1    Campbell, J.C.2    Whitten, S.T.3
  • 19
    • 4243127473 scopus 로고
    • Critical exponents for the n-vector model in three dimensions from field theory
    • LeGuillou JC, Zinn-Justin J. Critical exponents for the n-vector model in three dimensions from field theory. Phys Rev Lett 1977;39:95-98.
    • (1977) Phys Rev Lett , vol.39 , pp. 95-98
    • LeGuillou, J.C.1    Zinn-Justin, J.2
  • 20
    • 0025906282 scopus 로고
    • Polymer principles in protein structure and stability
    • Chan HS, Dill KA. Polymer principles in protein structure and stability. Annu Rev Biophys Biophys Chem 1991;20:447-490.
    • (1991) Annu Rev Biophys Biophys Chem , vol.20 , pp. 447-490
    • Chan, H.S.1    Dill, K.A.2
  • 21
    • 0017429069 scopus 로고
    • Areas, #volumes, |packing, and protein structure
    • Richards FM. Areas, #volumes, |packing, and protein structure. Annu Rev Biophys Bioeng 1977;6:151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 22
    • 0034700307 scopus 로고    scopus 로고
    • pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state
    • Whitten ST, García-Moreno EB. pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state. Biochemistry 2000;39:14292-14304.
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.T.1    García-Moreno, E.B.2
  • 23
    • 0002498995 scopus 로고
    • Computer-aided interpretation of analytical sedimentation data for proteins
    • Harding S, Rowe A, Horton JC, editors. UK: Royal Society of Chemistry;
    • Laue TM, Shah BD, Ridgeway TM, Pelletier SL. Computer-aided interpretation of analytical sedimentation data for proteins. In: Harding S, Rowe A, Horton JC, editors. Analytical Ultracentrifugation in Biochemistry and Polymer Science. UK: Royal Society of Chemistry; 1992. pp 90-125.
    • (1992) Analytical Ultracentrifugation in Biochemistry and Polymer Science , pp. 90-125
    • Laue, T.M.1    Shah, B.D.2    Ridgeway, T.M.3    Pelletier, S.L.4
  • 24
    • 46449135086 scopus 로고    scopus 로고
    • Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain
    • Whitten ST, Yang HW, Fox RO, Hilser VJ. Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain. Protein Sci 2008;17:1200-1211.
    • (2008) Protein Sci , vol.17 , pp. 1200-1211
    • Whitten, S.T.1    Yang, H.W.2    Fox, R.O.3    Hilser, V.J.4
  • 25
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
    • Momany FA, McGuire RF, Burgess AW, Scheraga HA. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J Phys Chem 1975;79:2361-2381.
    • (1975) J Phys Chem , vol.79 , pp. 2361-2381
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 26
    • 0017391163 scopus 로고
    • Tuna cytochrome c at 2.0 Å resolution. III. Coordinate optimization and comparison of structures
    • Mandel N, Mandel G, Trus BL, Rosenberg J, Carlson G, Dickerson RE. Tuna cytochrome c at 2.0 Å resolution. III. Coordinate optimization and comparison of structures. J Biol Chem 1977;252:4619-4636.
    • (1977) J Biol Chem , vol.252 , pp. 4619-4636
    • Mandel, N.1    Mandel, G.2    Trus, B.L.3    Rosenberg, J.4    Carlson, G.5    Dickerson, R.E.6
  • 27
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur MW, Thornton JM. Influence of proline residues on protein conformation. J Mol Biol 1991;218:397-412.
    • (1991) J Mol Biol , vol.218 , pp. 397-412
    • MacArthur, M.W.1    Thornton, J.M.2
  • 29
    • 0000180763 scopus 로고
    • Temperature dependence of the hydrophobic interaction in protein folding
    • Baldwin RL. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA 1986;83:8069-8072.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 8069-8072
    • Baldwin, R.L.1
  • 30
    • 0026756702 scopus 로고
    • Thermodynamics of structural stability and cooperative folding behavior in proteins
    • Murphy KP, Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem 1992;43:313-361.
    • (1992) Adv Protein Chem , vol.43 , pp. 313-361
    • Murphy, K.P.1    Freire, E.2
  • 31
    • 0026649261 scopus 로고
    • Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates
    • Murphy KP, Bhakuni V, Xie D, Freire E. Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates. J Mol Biol 1992;227:293-306.
    • (1992) J Mol Biol , vol.227 , pp. 293-306
    • Murphy, K.P.1    Bhakuni, V.2    Xie, D.3    Freire, E.4
  • 32
    • 0027991081 scopus 로고
    • Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation
    • Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 1994;20:68-84.
    • (1994) Proteins , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 33
    • 0028146012 scopus 로고
    • Structure based prediction of protein folding intermediates
    • Xie D, Freire E. Structure based prediction of protein folding intermediates. J Mol Biol 1994;242:62-80.
    • (1994) J Mol Biol , vol.242 , pp. 62-80
    • Xie, D.1    Freire, E.2
  • 35
  • 36
    • 0029941271 scopus 로고    scopus 로고
    • Energetics of hydrogen bonding in proteins: a model compound study
    • Habermann SM, Murphy KP. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci 1996;5:1229-1239.
    • (1996) Protein Sci , vol.5 , pp. 1229-1239
    • Habermann, S.M.1    Murphy, K.P.2
  • 37
    • 0029958659 scopus 로고    scopus 로고
    • Structure-based thermodynamic scale of alpha-helix propensities in amino acids
    • Luque I, Mayorga OL, Freire E. Structure-based thermodynamic scale of alpha-helix propensities in amino acids. Biochemistry 1996;35:13681-13688.
    • (1996) Biochemistry , vol.35 , pp. 13681-13688
    • Luque, I.1    Mayorga, O.L.2    Freire, E.3
  • 40
    • 0002251831 scopus 로고
    • Circular dichroism and conformation of unordered polypeptides
    • Woody RW. Circular dichroism and conformation of unordered polypeptides. Adv Biophys Chem 1992;2:37-79.
    • (1992) Adv Biophys Chem , vol.2 , pp. 37-79
    • Woody, R.W.1
  • 41
    • 0036129072 scopus 로고    scopus 로고
    • Polyproline II helical structure in protein unfolded states: lysine peptides revisited
    • Rucker AL, Creamer TP. Polyproline II helical structure in protein unfolded states: lysine peptides revisited. Protein Sci 2002;11:980-985.
    • (2002) Protein Sci , vol.11 , pp. 980-985
    • Rucker, A.L.1    Creamer, T.P.2
  • 42
    • 17644422781 scopus 로고    scopus 로고
    • Urea promotes polyproline II helix formation: implications for protein denatured states
    • Whittington SJ, Chellgren BW, Hermann VM, Creamer TP. Urea promotes polyproline II helix formation: implications for protein denatured states. Biochemistry 2005;44:6269-6275.
    • (2005) Biochemistry , vol.44 , pp. 6269-6275
    • Whittington, S.J.1    Chellgren, B.W.2    Hermann, V.M.3    Creamer, T.P.4
  • 43
    • 0025877987 scopus 로고
    • The crystal structure of Staphylococcal nuclease refined at 1.7-A resolution
    • Hynes TR, Fox RO. The crystal structure of Staphylococcal nuclease refined at 1.7-A resolution. Proteins 1991;10:92-105.
    • (1991) Proteins , vol.10 , pp. 92-105
    • Hynes, T.R.1    Fox, R.O.2
  • 44
    • 0026540830 scopus 로고
    • Purification and characterization of the carboxyl-terminal transactivation domain of Vmw65 from herpes simplex virus type 1
    • Donaldson L, Capone JP. Purification and characterization of the carboxyl-terminal transactivation domain of Vmw65 from herpes simplex virus type 1. J Biol Chem 1992;267:1411-1414.
    • (1992) J Biol Chem , vol.267 , pp. 1411-1414
    • Donaldson, L.1    Capone, J.P.2
  • 45
    • 74949125046 scopus 로고    scopus 로고
    • The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains
    • Richardson LG, Jelokhani-Niaraki M, Smith MD. The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains. BMC Biochem 2009;10:35.
    • (2009) BMC Biochem , vol.10 , pp. 35
    • Richardson, L.G.1    Jelokhani-Niaraki, M.2    Smith, M.D.3
  • 47
    • 0023505511 scopus 로고
    • Calibration of effective van der Waals atomic contact radii for proteins and peptides
    • Iijima H, Dunbar JB Jr, Marshall GR. Calibration of effective van der Waals atomic contact radii for proteins and peptides. Proteins 1987;2:330-339.
    • (1987) Proteins , vol.2 , pp. 330-339
    • Iijima, H.1    Dunbar Jr, J.B.2    Marshall, G.R.3
  • 48
    • 0033554852 scopus 로고    scopus 로고
    • Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques
    • Wilkins DK, Grimshaw SB, Receveur V, Dobson CM, Jones JA, Smith LJ. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry 1999;38:16424-16431.
    • (1999) Biochemistry , vol.38 , pp. 16424-16431
    • Wilkins, D.K.1    Grimshaw, S.B.2    Receveur, V.3    Dobson, C.M.4    Jones, J.A.5    Smith, L.J.6
  • 49
    • 33746882148 scopus 로고    scopus 로고
    • Metrics that differentiate the origins of osmolyte effects on protein stability: a test of the surface tension proposal
    • Auton M, Ferreon ACM, Bolen DW. Metrics that differentiate the origins of osmolyte effects on protein stability: a test of the surface tension proposal. J Mol Biol 2006;361:983-992.
    • (2006) J Mol Biol , vol.361 , pp. 983-992
    • Auton, M.1    Ferreon, A.C.M.2    Bolen, D.W.3
  • 50
    • 0000670923 scopus 로고
    • Structure of poly-l-proline
    • Cowan PM, McGavin S. Structure of poly-l-proline. Nature 1955;176:501-503.
    • (1955) Nature , vol.176 , pp. 501-503
    • Cowan, P.M.1    McGavin, S.2
  • 51
    • 0014364651 scopus 로고
    • Protein denaturation
    • Tanford C. Protein denaturation. Adv Protein Chem 1968;23:121-282.
    • (1968) Adv Protein Chem , vol.23 , pp. 121-282
    • Tanford, C.1
  • 52
    • 0014027356 scopus 로고
    • Proteins in 6-M guanidine hydrochloride. Demonstration of random coil behavior
    • Tanford C, Kawahara K, Lapanje S. Proteins in 6-M guanidine hydrochloride. Demonstration of random coil behavior. J Biol Chem 1966;241:1921-1923.
    • (1966) J Biol Chem , vol.241 , pp. 1921-1923
    • Tanford, C.1    Kawahara, K.2    Lapanje, S.3
  • 53
    • 0027733616 scopus 로고
    • Use of fast protein size-exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule
    • Uversky VN. Use of fast protein size-exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule. Biochemistry 1993;32:13288-13298.
    • (1993) Biochemistry , vol.32 , pp. 13288-13298
    • Uversky, V.N.1
  • 55
    • 77952335311 scopus 로고    scopus 로고
    • Net charge per residue modulates conformational ensembles of intrinsically disordered proteins
    • Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci USA 2010;107:8183-8188.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 8183-8188
    • Mao, A.H.1    Crick, S.L.2    Vitalis, A.3    Chicoine, C.L.4    Pappu, R.V.5
  • 56
    • 11144230087 scopus 로고    scopus 로고
    • A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)
    • Fleming PJ, Fitzkee NC, Mezei M, Srinivasan R, Rose GD. A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Sci 2005;14:111-118.
    • (2005) Protein Sci , vol.14 , pp. 111-118
    • Fleming, P.J.1    Fitzkee, N.C.2    Mezei, M.3    Srinivasan, R.4    Rose, G.D.5
  • 57
    • 78651105014 scopus 로고    scopus 로고
    • Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints
    • Porter LL, Rose GD. Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints. Proc Natl Acad Sci USA 2011;108:109-113.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 109-113
    • Porter, L.L.1    Rose, G.D.2
  • 59
    • 0019816864 scopus 로고
    • Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions
    • Artymiuk PJ, Blake CC. Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions. J Mol Biol 1981;152:737-762.
    • (1981) J Mol Biol , vol.152 , pp. 737-762
    • Artymiuk, P.J.1    Blake, C.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.