The Protein Folding Problem

作者: Ken A. Dill , S. Banu Ozkan , M. Scott Shell , Thomas R. Weikl

DOI: 10.1146/ANNUREV.BIOPHYS.37.092707.153558

关键词: ChemistryProtein structureProtein designComputational chemistryPeptide sequenceNative structureProtein structure predictionComputational biologyCASPProtein foldingProtein engineering

摘要: The “protein folding problem” consists of three closely related puzzles: (a) What is the code? (b) mechanism? (c) Can we predict native structure a protein from its amino acid sequence? Once regarded as grand challenge, has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely moving toward successful applications. structures small now often well predicted by computer methods. And, there testable explanation for how can fold so quickly: A solves large global optimization problem series smaller local problems, growing assembling peptide fragments, first.

参考文章(245)
Karen L. Maxwell, David Wildes, Arash Zarrine-Afsar, Miguel A. De Los Rios, Andrew G. Brown, Claire T. Friel, Linda Hedberg, Jia-Cherng Horng, Diane Bona, Erik J. Miller, Alexis Vallée-Bélisle, Ewan R.G. Main, Francesco Bemporad, Linlin Qiu, Kaare Teilum, Ngoc-Diep Vu, Aled M. Edwards, Ingo Ruczinski, Flemming M. Poulsen, Birthe B. Kragelund, Stephen W. Michnick, Fabrizio Chiti, Yawen Bai, Stephen J. Hagen, Luis Serrano, Mikael Oliveberg, Daniel P. Raleigh, Pernilla Wittung-Stafshede, Sheena E. Radford, Sophie E. Jackson, Tobin R. Sosnick, Susan Marqusee, Alan R. Davidson, Kevin W. Plaxco, Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Science. ,vol. 14, pp. 602- 616 ,(2005) , 10.1110/PS.041205405
Ken A. Dill, Polymer principles and protein folding. Protein Science. ,vol. 8, pp. 1166- 1180 ,(1999) , 10.1110/PS.8.6.1166
Kresten Lindorff-Larsen, Emanuele Paci, Luis Serrano, Christopher M. Dobson, Michele Vendruscolo, Calculation of Mutational Free Energy Changes in Transition States for Protein Folding Biophysical Journal. ,vol. 85, pp. 1207- 1214 ,(2003) , 10.1016/S0006-3495(03)74556-1
Richard Wolfenden, Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins The Journal of General Physiology. ,vol. 129, pp. 357- 362 ,(2007) , 10.1085/JGP.200709743
David Baker, Andrej Sali, Protein Structure Prediction and Structural Genomics Science. ,vol. 294, pp. 93- 96 ,(2001) , 10.1126/SCIENCE.1065659
Ken A. Dill, Adam Lucas, Julia Hockenmaier, Liang Huang, David Chiang, Aravind K. Joshi, Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics Polymer. ,vol. 48, pp. 4289- 4300 ,(2007) , 10.1016/J.POLYMER.2007.05.018
V. Munoz, J. M. Sanchez-Ruiz, Exploring protein-folding ensembles: A variable-barrier model for the analysis of equilibrium unfolding experiments Proceedings of the National Academy of Sciences of the United States of America. ,vol. 101, pp. 17646- 17651 ,(2004) , 10.1073/PNAS.0405829101
Marek Grabowski, Andrzej Joachimiak, Zbyszek Otwinowski, Wladek Minor, Structural genomics: keeping up with expanding knowledge of the protein universe Current Opinion in Structural Biology. ,vol. 17, pp. 347- 353 ,(2007) , 10.1016/J.SBI.2007.06.003
David A. Brant, P. J. Flory, The Role of Dipole Interactions in Determining Polypeptide Configurations Journal of the American Chemical Society. ,vol. 87, pp. 663- 664 ,(1965) , 10.1021/JA01081A054
Lei Wang, Jianming Xie, Peter G. Schultz, Expanding the genetic code. Annual Review of Biophysics and Biomolecular Structure. ,vol. 35, pp. 225- 249 ,(2006) , 10.1146/ANNUREV.BIOPHYS.35.101105.121507