메뉴 건너뛰기




Volumn 54, Issue 9, 2015, Pages 1758-1766

Fast helix formation in the b domain of protein a revealed by site-specific infrared probes

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; INFRARED SPECTROSCOPY; ISOTOPES; PEPTIDES; PROBES; PROTEIN FOLDING; PROTEINS;

EID: 84924362914     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b00037     Document Type: Article
Times cited : (31)

References (37)
  • 2
    • 83755162489 scopus 로고    scopus 로고
    • Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes
    • Nagarajan, S., Taskent-Sezgin, H., Parul, D., Carrico, I., Raleigh, D. P., and Dyer, R. B. (2011) Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes J. Am. Chem. Soc. 133, 20335-20340
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 20335-20340
    • Nagarajan, S.1    Taskent-Sezgin, H.2    Parul, D.3    Carrico, I.4    Raleigh, D.P.5    Dyer, R.B.6
  • 3
    • 33947413082 scopus 로고    scopus 로고
    • Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy
    • Brewer, S. H., Song, B., Raleigh, D. P., and Dyer, R. B. (2007) Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy Biochemistry 46, 3279-3285
    • (2007) Biochemistry , vol.46 , pp. 3279-3285
    • Brewer, S.H.1    Song, B.2    Raleigh, D.P.3    Dyer, R.B.4
  • 4
    • 79952332935 scopus 로고    scopus 로고
    • Carbon-deuterium bonds as site-specific and nonperturbative probes for time-resolved studies of protein dynamics and folding
    • Zimmermann, J., Thielges, M. C., Yu, W., Dawson, P. E., and Romesberg, F. E. (2011) Carbon-deuterium bonds as site-specific and nonperturbative probes for time-resolved studies of protein dynamics and folding J. Phys. Chem. Lett. 2, 412-416
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 412-416
    • Zimmermann, J.1    Thielges, M.C.2    Yu, W.3    Dawson, P.E.4    Romesberg, F.E.5
  • 5
    • 34547651105 scopus 로고    scopus 로고
    • Searching for multiple folding pathways of a nearly symmetrical protein: Temperature dependent -value analysis of the B domain of protein A
    • Sato, S. and Fersht, A. R. (2007) Searching for multiple folding pathways of a nearly symmetrical protein: Temperature dependent -value analysis of the B domain of protein A J. Mol. Biol. 372, 254-267
    • (2007) J. Mol. Biol. , vol.372 , pp. 254-267
    • Sato, S.1    Fersht, A.R.2
  • 6
    • 2342449128 scopus 로고    scopus 로고
    • Testing protein-folding simulations by experiment: B domain of protein A
    • Sato, S., Religa, T. L., Daggett, V., and Fersht, A. R. (2004) Testing protein-folding simulations by experiment: B domain of protein A Proc. Natl. Acad. Sci. U.S.A. 101, 6952-6956
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 6952-6956
    • Sato, S.1    Religa, T.L.2    Daggett, V.3    Fersht, A.R.4
  • 7
    • 48749087319 scopus 로고    scopus 로고
    • Quantifying the structural requirements of the folding transition state of protein A and other systems
    • Baxa, M. C., Freed, K. F., and Sosnick, T. R. (2008) Quantifying the structural requirements of the folding transition state of protein A and other systems J. Mol. Biol. 381, 1362-1381
    • (2008) J. Mol. Biol. , vol.381 , pp. 1362-1381
    • Baxa, M.C.1    Freed, K.F.2    Sosnick, T.R.3
  • 8
    • 84882789896 scopus 로고    scopus 로고
    • 3.3 fast events in protein folding
    • In (Egelman, E. H. Ed.) pp, Elsevier, Amsterdam
    • Dyer, R. B. and Vu, D. M. (2012) 3.3 fast events in protein folding. In Comprehensive biophysics (Egelman, E. H., Ed.) pp 34-42, Elsevier, Amsterdam.
    • (2012) Comprehensive Biophysics , pp. 34-42
    • Dyer, R.B.1    Vu, D.M.2
  • 9
    • 2542548801 scopus 로고    scopus 로고
    • Experimental resolution of early steps in protein folding: Testing molecular dynamics simulations
    • Vu, D. M., Peterson, E. S., and Dyer, R. B. (2004) Experimental resolution of early steps in protein folding: Testing molecular dynamics simulations J. Am. Chem. Soc. 126, 6546-6547
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 6546-6547
    • Vu, D.M.1    Peterson, E.S.2    Dyer, R.B.3
  • 10
    • 1642414760 scopus 로고    scopus 로고
    • Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein
    • Vu, D. M., Myers, J. K., Oas, T. G., and Dyer, R. B. (2004) Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein Biochemistry 43, 3582-3589
    • (2004) Biochemistry , vol.43 , pp. 3582-3589
    • Vu, D.M.1    Myers, J.K.2    Oas, T.G.3    Dyer, R.B.4
  • 11
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
    • Garcia, A. E. and Onuchic, J. N. (2003) Folding a protein in a computer: An atomic description of the folding/unfolding of protein A Proc. Natl. Acad. Sci. U.S.A. 100, 13898-13903
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 13898-13903
    • Garcia, A.E.1    Onuchic, J.N.2
  • 12
    • 0030967896 scopus 로고    scopus 로고
    • Exploring the folding free energy surface of a three-helix bundle protein
    • Guo, Z., Brooks, C. L., III, and Boczko, E. M. (1997) Exploring the folding free energy surface of a three-helix bundle protein Proc. Natl. Acad. Sci. U.S.A. 94, 10161-10166
    • (1997) Proc. Natl. Acad. Sci. U.S.A. , vol.94 , pp. 10161-10166
    • Guo, Z.1    Brooks, C.L.2    Boczko, E.M.3
  • 13
    • 30544431715 scopus 로고    scopus 로고
    • Transition state ensemble for the folding of B domain of protein A: A comparison of distributed molecular dynamics simulations with experiments
    • Cheng, S., Yang, Y., Wang, W., and Liu, H. (2005) Transition state ensemble for the folding of B domain of protein A: A comparison of distributed molecular dynamics simulations with experiments J. Phys. Chem. B 109, 23645-23654
    • (2005) J. Phys. Chem. B , vol.109 , pp. 23645-23654
    • Cheng, S.1    Yang, Y.2    Wang, W.3    Liu, H.4
  • 14
    • 0034602807 scopus 로고    scopus 로고
    • Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and e domains
    • Alonso, D. O. and Daggett, V. (2000) Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains Proc. Natl. Acad. Sci. U.S.A. 97, 133-138
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 133-138
    • Alonso, D.O.1    Daggett, V.2
  • 15
    • 0028326042 scopus 로고
    • Monte Carlo simulations of protein folding. II. Application to protein A, rop, and crambin
    • Kolinski, A. and Skolnick, J. (1994) Monte Carlo simulations of protein folding. II. Application to protein A, rop, and crambin Proteins 18, 353-366
    • (1994) Proteins , vol.18 , pp. 353-366
    • Kolinski, A.1    Skolnick, J.2
  • 16
    • 0036678831 scopus 로고    scopus 로고
    • An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
    • Ghosh, A., Elber, R., and Scheraga, H. A. (2002) An atomically detailed study of the folding pathways of protein A with the stochastic difference equation Proc. Natl. Acad. Sci. U.S.A. 99, 10394-10398
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 10394-10398
    • Ghosh, A.1    Elber, R.2    Scheraga, H.A.3
  • 17
    • 80054711003 scopus 로고    scopus 로고
    • The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation
    • Shao, Q. and Gao, Y. Q. (2011) The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation J. Chem. Phys. 135, 135102
    • (2011) J. Chem. Phys. , vol.135 , pp. 135102
    • Shao, Q.1    Gao, Y.Q.2
  • 18
    • 84901992662 scopus 로고    scopus 로고
    • Probing sequence dependence of folding pathway of -helix bundle proteins through free energy landscape analysis
    • Shao, Q. (2014) Probing sequence dependence of folding pathway of -helix bundle proteins through free energy landscape analysis J. Phys. Chem. B 118, 5891-5900
    • (2014) J. Phys. Chem. B , vol.118 , pp. 5891-5900
    • Shao, Q.1
  • 19
    • 47249119770 scopus 로고    scopus 로고
    • Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
    • Lei, H., Wu, C., Wang, Z. X., Zhou, Y., and Duan, Y. (2008) Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations J. Chem. Phys. 128, 235105
    • (2008) J. Chem. Phys. , vol.128 , pp. 235105
    • Lei, H.1    Wu, C.2    Wang, Z.X.3    Zhou, Y.4    Duan, Y.5
  • 20
    • 65249086776 scopus 로고    scopus 로고
    • Time-resolved fluorescence resonance energy transfer study shows a compact denatured state of the B domain of protein A
    • Huang, F., Lerner, E., Sato, S., Amir, D., Haas, E., and Fersht, A. R. (2009) Time-resolved fluorescence resonance energy transfer study shows a compact denatured state of the B domain of protein A Biochemistry 48, 3468-3476
    • (2009) Biochemistry , vol.48 , pp. 3468-3476
    • Huang, F.1    Lerner, E.2    Sato, S.3    Amir, D.4    Haas, E.5    Fersht, A.R.6
  • 21
    • 1642290710 scopus 로고    scopus 로고
    • Microsecond folding dynamics of the f13w g29a mutant of the B domain of staphylococcal protein A by laser-induced temperature jump
    • Dimitriadis, G., Drysdale, A., Myers, J. K., Arora, P., Radford, S. E., Oas, T. G., and Smith, D. A. (2004) Microsecond folding dynamics of the f13w g29a mutant of the B domain of staphylococcal protein A by laser-induced temperature jump Proc. Natl. Acad. Sci. U.S.A. 101, 3809-3814
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 3809-3814
    • Dimitriadis, G.1    Drysdale, A.2    Myers, J.K.3    Arora, P.4    Radford, S.E.5    Oas, T.G.6    Smith, D.A.7
  • 22
    • 1842454986 scopus 로고    scopus 로고
    • Fast and faster: A designed variant of the B-domain of protein A folds in 3 s
    • Arora, P., Oas, T. G., and Myers, J. K. (2004) Fast and faster: A designed variant of the B-domain of protein A folds in 3 s Protein Sci. 13, 847-853
    • (2004) Protein Sci. , vol.13 , pp. 847-853
    • Arora, P.1    Oas, T.G.2    Myers, J.K.3
  • 23
    • 36849050249 scopus 로고    scopus 로고
    • 18O-labeled Fmoc-amino acids with high levels of enrichment: Applications to isotope-edited IR studies of proteins
    • 18O-labeled Fmoc-amino acids with high levels of enrichment: Applications to isotope-edited IR studies of proteins Org. Lett. 9, 4935-4937
    • (2007) Org. Lett. , vol.9 , pp. 4935-4937
    • Marecek, J.1    Song, B.2    Brewer, S.3    Belyea, J.4    Dyer, R.B.5    Raleigh, D.P.6
  • 24
    • 0001324390 scopus 로고
    • Protein secondary structure from ft-ir spectroscopy: Correlation with dihedral angles from 3-dimensional Ramachandran plots
    • Jackson, M. and Mantsch, H. H. (1991) Protein secondary structure from ft-ir spectroscopy: Correlation with dihedral angles from 3-dimensional Ramachandran plots Can. J. Chem. 69, 1639-1642
    • (1991) Can. J. Chem. , vol.69 , pp. 1639-1642
    • Jackson, M.1    Mantsch, H.H.2
  • 26
    • 0023428747 scopus 로고
    • Theoretical determination of the CD of proteins containing closely packed antiparallel β-sheets
    • Manning, M. C. and Woody, R. W. (1987) Theoretical determination of the CD of proteins containing closely packed antiparallel β-sheets Biopolymers 26, 1731-1752
    • (1987) Biopolymers , vol.26 , pp. 1731-1752
    • Manning, M.C.1    Woody, R.W.2
  • 27
    • 0022024822 scopus 로고
    • Protein conformation by infrared-spectroscopy: Resolution enhancement by fourier self-deconvolution
    • Yang, W. J., Griffiths, P. R., Byler, D. M., and Susi, H. (1985) Protein conformation by infrared-spectroscopy: Resolution enhancement by fourier self-deconvolution Appl. Spectrosc. 39, 282-287
    • (1985) Appl. Spectrosc. , vol.39 , pp. 282-287
    • Yang, W.J.1    Griffiths, P.R.2    Byler, D.M.3    Susi, H.4
  • 28
    • 0029916233 scopus 로고    scopus 로고
    • Infrared evidence of a β-hairpin peptide structure in solution
    • Arrondo, J. L. R., Blanco, F. J., Serrano, L., and Goni, F. M. (1996) Infrared evidence of a β-hairpin peptide structure in solution FEBS Lett. 384, 35-37
    • (1996) FEBS Lett. , vol.384 , pp. 35-37
    • Arrondo, J.L.R.1    Blanco, F.J.2    Serrano, L.3    Goni, F.M.4
  • 29
    • 0022463740 scopus 로고
    • Resolution-enhanced fourier-transform infrared-spectroscopy of enzymes
    • Susi, H. and Byler, D. M. (1986) Resolution-enhanced fourier-transform infrared-spectroscopy of enzymes Methods Enzymol. 130, 290-311
    • (1986) Methods Enzymol. , vol.130 , pp. 290-311
    • Susi, H.1    Byler, D.M.2
  • 32
    • 0036880493 scopus 로고    scopus 로고
    • What vibrations tell us about proteins
    • Barth, A. and Zscherp, C. (2002) What vibrations tell us about proteins Q. Rev. Biophys. 35, 369-430
    • (2002) Q. Rev. Biophys. , vol.35 , pp. 369-430
    • Barth, A.1    Zscherp, C.2
  • 33
    • 33847754276 scopus 로고    scopus 로고
    • Infrared and vibrational CD spectra of partially solvated -helices: DFT-based simulations with explicit solvent
    • Turner, D. R. and Kubelka, J. (2007) Infrared and vibrational CD spectra of partially solvated -helices: DFT-based simulations with explicit solvent J. Phys. Chem. B 111, 1834-1845
    • (2007) J. Phys. Chem. B , vol.111 , pp. 1834-1845
    • Turner, D.R.1    Kubelka, J.2
  • 34
  • 35
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • Myers, J. K. and Oas, T. G. (2001) Preorganized secondary structure as an important determinant of fast protein folding Nat. Struct. Biol. 8, 552-558
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 36
    • 0036307683 scopus 로고    scopus 로고
    • Application of the diffusion-collision model to the folding of three-helix bundle proteins
    • Islam, S. A., Karplus, M., and Weaver, D. L. (2002) Application of the diffusion-collision model to the folding of three-helix bundle proteins J. Mol. Biol. 318, 199-215
    • (2002) J. Mol. Biol. , vol.318 , pp. 199-215
    • Islam, S.A.1    Karplus, M.2    Weaver, D.L.3
  • 37
    • 33847229871 scopus 로고    scopus 로고
    • Local structure formation in simulations of two small proteins
    • Jayachandran, G., Vishal, V., Garcia, A. E., and Pande, V. S. (2007) Local structure formation in simulations of two small proteins J. Struct. Biol. 157, 491-499
    • (2007) J. Struct. Biol. , vol.157 , pp. 491-499
    • Jayachandran, G.1    Vishal, V.2    Garcia, A.E.3    Pande, V.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.