Sub-microsecond Protein Folding

Data Reduction and Error Analysis for the Physical Sciences

Bevington, P. R., Robinson, D. K., Blair, J. M., Mallinckrodt, A. J., & McKay, S. (1993) · Computers in Physics · doi:10.1063/1.4823194 · Cited by 14,824

Brownian motion in a field of force and the diffusion model of chemical reactions

Kramers, H. A. (1940) · Physica · doi:10.1016/s0031-8914(40)90098-2 · Cited by 8,625

Funnels, pathways, and the energy landscape of protein folding: A synthesis

Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648

The protein folding ‘speed limit’

Kubelka, J., Hofrichter, J., & Eaton, W. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.01.013 · Cited by 830

Absolute comparison of simulated and experimental protein-folding dynamics

Snow, C. D., Nguyen, H., Pande, V. S., & Gruebele, M. (2002) · Nature · doi:10.1038/nature01160 · Cited by 701

Fast Kinetics and Mechanisms in Protein Folding

Eaton, W. A., Muñoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R., & Hofrichter, J. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.327 · Cited by 488

The complete folding pathway of a protein from nanoseconds to microseconds

Mayor, U., Guydosh, N. R., Johnson, C. M., Grossmann, J. G., Sato, S., Jas, G. S., Freund, S. M. V., Alonso, D. O. V., Daggett, V., & Fersht, A. R. (2003) · Nature · doi:10.1038/nature01428 · Cited by 458

Classical and modern methods in reaction rate theory

Berne, B. J., Borkovec, M., & Straub, J. E. (1988) · The Journal of Physical Chemistry · doi:10.1021/j100324a007 · Cited by 409

Measuring the rate of intramolecular contact formation in polypeptides

Lapidus, L. J., Eaton, W. A., & Hofrichter, J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.7220 · Cited by 409

Folding at the speed limit

Yang, W. Y., & Gruebele, M. (2003) · Nature · doi:10.1038/nature01609 · Cited by 401

Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding.

Hagen, S. J., Hofrichter, J., Szabo, A., & Eaton, W. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11615 · Cited by 400

Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs

Qiu, L., Pabit, S. A., Roitberg, A. E., & Hagen, S. J. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0279141 · Cited by 333

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation

Mayor, U., Johnson, C. M., Daggett, V., & Fersht, A. R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.250473497 · Cited by 316

Observation of strange kinetics in protein folding

Sabelko, J., Ervin, J., & Gruebele, M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.11.6031 · Cited by 310

Experimental Identification of Downhill Protein Folding

Garcia-Mira, M. M., Sadqi, M., Fischer, N., Sanchez-Ruiz, J. M., & Muñoz, V. (2002) · Science · doi:10.1126/science.1077809 · Cited by 307

Fast events in protein folding initiated by nanosecond laser photolysis.

Jones, C. M., Henry, E. R., Hu, Y., Chan, C. K., Luck, S. D., Bhuyan, A., Roder, H., Hofrichter, J., & Eaton, W. A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.24.11860 · Cited by 306

Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing

Zagrovic, B., Snow, C. D., Shirts, M. R., & Pande, V. S. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00997-x · Cited by 286

Experimental Tests of Villin Subdomain Folding Simulations

Kubelka, J., Eaton, W. A., & Hofrichter, J. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00519-9 · Cited by 240

How Well Can Simulation Predict Protein Folding Kinetics and Thermodynamics?

Snow, C. D., Sorin, E. J., Rhee, Y. M., & Pande, V. S. (2005) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.34.040204.144447 · Cited by 236

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

Chiu, T. K., Kubelka, J., Herbst-Irmer, R., Eaton, W. A., Hofrichter, J., & Davies, D. R. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502495102 · Cited by 224

Preorganized secondary structure as an important determinant of fast protein folding.

Myers, J. K., & Oas, T. G. (2001) · Nature Structural Biology · doi:10.1038/88626 · Cited by 215

FAST EVENTS IN PROTEIN FOLDING: The Time Evolution of Primary Processes

Callender, R. H., Dyer, R. B., Gilmanshin, R., & Woodruff, W. H. (1998) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.49.1.173 · Cited by 205

T HE F AST P ROTEIN F OLDING P ROBLEM

Gruebele, M. (1999) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.50.1.485 · Cited by 203

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

Snow, C. D., Qiu, L., Du, D., Gai, F., Hagen, S. J., & Pande, V. S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0305260101 · Cited by 184

Ultrafast folding of α 3 D: A de novo designed three-helix bundle protein

Zhu, Y., Alonso, D. O. V., Maki, K., Huang, C., Lahr, S. J., Daggett, V., Röder, H., DeGrado, W. F., & Gai, F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2136623100 · Cited by 153

Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation

Nguyen, H., Jäger, M., Moretto, A., Gruebele, M., & Kelly, J. W. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0538054100 · Cited by 148

Dynamic NMR Line-Shape Analysis Demonstrates that the Villin Headpiece Subdomain Folds on the Microsecond Time Scale

Wang, M., Tang, Y., Sato, S., Vugmeyster, L., McKnight, C. J., & Raleigh, D. P. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028752b · Cited by 122

Mechanisms of Fast Protein Folding

Myers, J. K., & Oas, T. G. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135346 · Cited by 115

Ultra-fast Barrier-limited Folding in the Peripheral Subunit-binding Domain Family

Ferguson, N. S., Sharpe, T., Schartau, P. J., Sato, S., Allen, M. D., Johnson, C. M., Rutherford, T. J., & Fersht, A. R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.08.031 · Cited by 106

Folding λ-Repressor at Its Speed Limit

Yang, W. Y., & Gruebele, M. (2004) · Biophysical Journal · doi:10.1529/biophysj.103.039040 · Cited by 103

Ultrafast folding of WW domains without structured aromatic clusters in the denatured state

Ferguson, N. S., Johnson, C. M., Macías, M. J., Oschkinat, H., & Fersht, A. R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.221467198 · Cited by 102

Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides

Buscaglia, M., Lapidus, L. J., Eaton, W. A., & Hofrichter, J. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.071167 · Cited by 100

Searching for “downhill scenarios” in protein folding

Eaton, W. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.11.5897 · Cited by 99

Kinetics are probe-dependent during downhill folding of an engineered λ 6–85 protein

Ma, H., & Gruebele, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409270102 · Cited by 93

Robustness of Downhill Folding: Guidelines for the Analysis of Equilibrium Folding Experiments on Small Proteins

Naganathan, A. N., Pérez‐Jiménez, R., Sánchez‐Ruiz, J. M., & Muñoz, V. (2005) · Biochemistry · doi:10.1021/bi050118y · Cited by 84

Engineering a β-Sheet Protein toward the Folding Speed Limit

Nguyen, H., Jäger, M., Kelly, J. W., & Gruebele, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp052373y · Cited by 63

Photoacoustic cavitation and heat transfer effects in the laser-induced temperature jump in water

Wray, W. O., Aida, T., & Dyer, R. B. (2002) · Applied Physics B · doi:10.1007/s003400100752 · Cited by 62

Kinetics of Intramolecular Contact Formation in a Denatured Protein

Buscaglia, M., Schuler, B., Lapidus, L. J., Eaton, W. A., & Hofrichter, J. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00891-x · Cited by 59

Large-Scale Context in Protein Folding: Villin Headpiece

Fernández, A., Shen, M., Colubri, A., Sosnick, T. R., Berry, R. S., & Freed, K. F. (2003) · Biochemistry · doi:10.1021/bi026510i · Cited by 54

Guiding the search for a protein's maximum rate of folding

Zhu, Y., Fu, X., Wang, T., Tamura, A., Takada, S., Saven, J. G., & Gai, F. (2004) · Chemical Physics · doi:10.1016/j.chemphys.2004.05.008 · Cited by 50

Diffusional limits to the speed of protein folding: fact or friction?

Hagen, S. J., Qiu, L., & Pabit, S. A. (2005) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/17/18/008 · Cited by 47

Internal friction in the ultrafast folding of the tryptophan cage

Qiu, L., & Hagen, S. J. (2004) · Chemical Physics · doi:10.1016/j.chemphys.2004.12.002 · Cited by 47

Internal friction in the ultrafast folding of the tryptophan cage

Qiu, L., & Hagen, S. J. (2004) · Chemical Physics · doi:10.1016/j.chemphys.2004.04.030 · Cited by 20

How fast-folding proteins fold

Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980

Atomic-level characterization of the structural dynamics of proteins

Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., et al. (2010) · Science · doi:10.1126/science.1187409 · Cited by 1,923

The Protein Folding Problem

Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

Piana, S., Klepeis, J. L., & Shaw, D. E. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.12.006 · Cited by 512

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)

Voelz, V. A., Bowman, G. R., Beauchamp, K., & Pande, V. S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja9090353 · Cited by 503