An exciting but challenging road ahead for computational enzyme design

作者: David Baker

DOI: 10.1002/PRO.481

关键词: NanotechnologyBiochemical engineeringComputational designComputer science

摘要: … We believe computational enzyme design has tremendous potential for a wide range of important applications and to illuminate fundamental issues in catalysis. To achieve these ends, …

参考文章(14)
Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker, Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Science. ,vol. 302, pp. 1364- 1368 ,(2003) , 10.1126/SCIENCE.1089427
Daniela Röthlisberger, Olga Khersonsky, Andrew M. Wollacott, Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker, Kemp elimination catalysts by computational enzyme design Nature. ,vol. 453, pp. 190- 195 ,(2008) , 10.1038/NATURE06879
Adam JT Smith, Roger Müller, Miguel D Toscano, Peter Kast, Homme W Hellinga, Donald Hilvert, KN Houk, None, Structural Reorganization and Preorganization in Enzyme Active Sites: Comparisons of Experimental and Theoretically Ideal Active Site Geometries in the Multistep Serine Esterase Reaction Cycle Journal of the American Chemical Society. ,vol. 130, pp. 15361- 15373 ,(2008) , 10.1021/JA803213P
Richard Wolfenden, Mark J. Snider, The Depth of Chemical Time and the Power of Enzymes as Catalysts Accounts of Chemical Research. ,vol. 34, pp. 938- 945 ,(2001) , 10.1021/AR000058I
Jianhan Chen, Wonpil Im, Charles L. Brooks, Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field Journal of the American Chemical Society. ,vol. 128, pp. 3728- 3736 ,(2006) , 10.1021/JA057216R
Shimon Bershtein, Dan S Tawfik, Advances in laboratory evolution of enzymes. Current Opinion in Chemical Biology. ,vol. 12, pp. 151- 158 ,(2008) , 10.1016/J.CBPA.2008.01.027
Anthony K. Mittermaier, Lewis E. Kay, Observing biological dynamics at atomic resolution using NMR Trends in Biochemical Sciences. ,vol. 34, pp. 601- 611 ,(2009) , 10.1016/J.TIBS.2009.07.004
Orlando Acevedo, William L. Jorgensen, Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Accounts of Chemical Research. ,vol. 43, pp. 142- 151 ,(2010) , 10.1021/AR900171C
Vladimir Hnizdo, Jun Tan, Benjamin J. Killian, Michael K. Gilson, Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods Journal of Computational Chemistry. ,vol. 29, pp. 1605- 1614 ,(2008) , 10.1002/JCC.20919
Andreas Heine, John G. Luz, Chi-Huey Wong, Ian A. Wilson, Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution. Journal of Molecular Biology. ,vol. 343, pp. 1019- 1034 ,(2004) , 10.1016/J.JMB.2004.08.066