The effect of surface tethering on the folding of the src-SH3 protein domain
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Joan-Emma Shea | Zhuoyun Zhuang | J. Shea | A. Jewett | Andrew I Jewett | Patricia Soto | Patricia Soto | Zhuoyun Zhuang
[1] X. Zhuang,et al. A single-molecule study of RNA catalysis and folding. , 2000, Science.
[2] W. Eaton,et al. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy , 2002, Nature.
[3] D. Lilley,et al. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. , 2004, Biophysical journal.
[4] David Baker,et al. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain , 1998, Nature Structural &Molecular Biology.
[5] Feng Ding,et al. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. , 2005, Journal of molecular biology.
[6] H. Chan,et al. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding , 2008, Proceedings of the National Academy of Sciences.
[7] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[8] G. Nienhaus,et al. Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis , 2007, Nucleic acids research.
[9] Joan-Emma Shea,et al. Probing the folding free energy landscape of the src-SH3 protein domain , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[10] L. Kay,et al. Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR. , 2006, Biochemistry.
[11] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[12] C L Brooks,et al. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[13] D Baker,et al. Circularization changes the folding transition state of the src SH3 domain. , 2001, Journal of molecular biology.
[14] Peter G Wolynes,et al. P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[15] R N Zare,et al. Probing individual molecules with confocal fluorescence microscopy. , 1994, Science.
[16] Hironori K. Nakamura,et al. Transition state of a SH3 domain detected with principle component analysis and a charge‐neutralized all‐atom protein model , 2006, Proteins.
[17] Juan J de Pablo,et al. Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. , 2006, Biophysical journal.
[18] M Wilmanns,et al. Solvation in protein folding analysis: combination of theoretical and experimental approaches. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[19] S. Weiss,et al. Single-molecule fluorescence studies of protein folding and conformational dynamics. , 2006, Chemical reviews.
[20] Hongtao Yu,et al. 1H and 15N assignments and secondary structure of the Src SH3 domain , 1993, FEBS letters.
[21] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[22] José N Onuchic,et al. Probing the kinetics of single molecule protein folding. , 2004, Biophysical journal.
[23] A. Caflisch,et al. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. , 2004, Biophysical Journal.
[24] C. Röcker,et al. Biofunctionalized polymer surfaces exhibiting minimal interaction towards immobilized proteins. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.
[25] D Baker,et al. Folding dynamics of the src SH3 domain. , 1997, Biochemistry.
[26] Shimon Weiss,et al. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy , 2000, Nature Structural Biology.
[27] David Baker,et al. Experiment and theory highlight role of native state topology in SH3 folding , 1999, Nature Structural Biology.
[28] Xiangxu Kong,et al. Single-molecule FRET reveals sugar-induced conformational dynamics in LacY , 2007, Proceedings of the National Academy of Sciences.
[29] T. Ha,et al. Single-molecule fluorescence resonance energy transfer. , 2001, Methods.
[30] Xiaowei Zhuang,et al. Single-molecule RNA folding. , 2005, Accounts of chemical research.
[31] L. Kay,et al. Characterization of the hydrodynamic properties of the folding transition state of an SH3 domain by magnetization transfer NMR spectroscopy. , 2006, Biochemistry.
[32] Katja Petzold,et al. Folding of the alphaII-spectrin SH3 domain under physiological salt conditions. , 2008, Archives of biochemistry and biophysics.
[33] Taekjip Ha,et al. Surfaces and orientations: much to FRET about? , 2004, Accounts of chemical research.
[34] Lydia E Kavraki,et al. From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes , 2007, Proteins.
[35] Jie Chen,et al. Transition states for folding of circular‐permuted proteins , 2004, Proteins.
[36] X. Zhuang. Single-molecule RNA science. , 2005, Annual review of biophysics and biomolecular structure.
[37] J. Onuchic,et al. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[38] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[39] S. Weiss. Fluorescence spectroscopy of single biomolecules. , 1999, Science.
[40] Alan M. Ferrenberg,et al. Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.
[41] T. Ha,et al. Single-molecule fluorescence methods for the study of nucleic acids. , 2001, Current opinion in structural biology.
[42] J. Johnson,et al. Amphitropic proteins: regulation by reversible membrane interactions (review). , 1999, Molecular membrane biology.
[43] H E Stanley,et al. Parallel folding pathways in the SH3 domain protein. , 2007, Journal of molecular biology.
[44] Eugene I Shakhnovich,et al. Nucleation and the transition state of the SH3 domain. , 2005, Journal of molecular biology.
[45] D Baker,et al. Long-range order in the src SH3 folding transition state. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[46] J. Onuchic,et al. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.
[47] Temperature dependence of the free energy landscape of the src‐SH3 protein domain , 2004, Proteins.
[48] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[49] A. Baumketner,et al. Stability of a protein tethered to a surface. , 2007, The Journal of chemical physics.
[50] S. Lampoudi,et al. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. , 2003, Biophysical journal.
[51] Everett A Lipman,et al. Single-Molecule Measurement of Protein Folding Kinetics , 2003, Science.
[52] Nitin Rathore,et al. An entropic perspective of protein stability on surfaces. , 2008, Biophysical journal.
[53] A. Baumketner,et al. Effects of surface tethering on protein folding mechanisms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.