High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design

[1]  David Baker,et al.  High-resolution structural validation of the computational redesign of human U1A protein. , 2006, Structure.

[2]  Guangfu Yang,et al.  Computational redesign of human butyrylcholinesterase for anticocaine medication. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. Bradley,et al.  Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.

[4]  B. Stoddard,et al.  Computational Thermostabilization of an Enzyme , 2005, Science.

[5]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[6]  Edo Kussell,et al.  The designability hypothesis and protein evolution. , 2005, Protein and peptide letters.

[7]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[8]  Loren L Looger,et al.  Computational Design of a Biologically Active Enzyme , 2004, Science.

[9]  David Baker,et al.  Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. , 2004, Journal of molecular biology.

[10]  D. Baker,et al.  Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.

[11]  David Baker,et al.  Exploring folding free energy landscapes using computational protein design. , 2004, Current opinion in structural biology.

[12]  Peter Güntert,et al.  Automated NMR protein structure calculation , 2003 .

[13]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[14]  Eugene A Zhukovsky,et al.  Inactivation of TNF Signaling by Rationally Designed Dominant-Negative TNF Variants , 2003, Science.

[15]  D. Baker,et al.  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. , 2003, Journal of molecular biology.

[16]  L. Looger,et al.  Computational design of receptor and sensor proteins with novel functions , 2003, Nature.

[17]  D. Baker,et al.  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.

[18]  Thomas C Terwilliger,et al.  SOLVE and RESOLVE: automated structure solution and density modification. , 2003, Methods in enzymology.

[19]  Sarah A. Teichmann,et al.  Principles of protein-protein interactions , 2002, ECCB.

[20]  Christopher T. Saunders,et al.  Evaluation of structural and evolutionary contributions to deleterious mutation prediction. , 2002, Journal of molecular biology.

[21]  Anirban Kundu,et al.  Computational stabilization of human growth hormone , 2002, Protein science : a publication of the Protein Society.

[22]  Z. Xiang,et al.  Extending the accuracy limits of prediction for side-chain conformations. , 2001, Journal of molecular biology.

[23]  C. Vita,et al.  Engineering novel bioactive mini-proteins from small size natural and de novo designed scaffolds. , 2000, Current protein & peptide science.

[24]  D. Baker,et al.  A surprising simplicity to protein folding , 2000, Nature.

[25]  L Serrano,et al.  Protein engineering as a strategy to avoid formation of amyloid fibrils , 2000, Protein science : a publication of the Protein Society.

[26]  B. Dahiyat,et al.  In silico design for protein stabilization. , 1999, Current opinion in biotechnology.

[27]  M. Karplus,et al.  Effective energy function for proteins in solution , 1999, Proteins.

[28]  D E McRee,et al.  XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. , 1999, Journal of structural biology.

[29]  Christian Griesinger,et al.  Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients , 1999 .

[30]  A. Bax,et al.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology , 1999, Journal of biomolecular NMR.

[31]  Christopher M. Summa,et al.  De novo design and structural characterization of proteins and metalloproteins. , 1999, Annual review of biochemistry.

[32]  D. Baker,et al.  Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins , 1999, Proteins.

[33]  P. S. Kim,et al.  High-resolution protein design with backbone freedom. , 1998, Science.

[34]  V. Krishnan,et al.  An empirical relationship between rotational correlation time and solvent accessible surface area , 1998, Journal of biomolecular NMR.

[35]  H. W. Hellinga,et al.  Computational protein engineering , 1998, Nature Structural Biology.

[36]  F. Avilés,et al.  The three‐dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen , 1997, The EMBO journal.

[37]  S. L. Mayo,et al.  De novo protein design: fully automated sequence selection. , 1997, Science.

[38]  Roland L. Dunbrack,et al.  Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.

[39]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[40]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[41]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[42]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[43]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[44]  A. Palmer,et al.  Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. , 1995, Journal of molecular biology.

[45]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[46]  G. Sheldrick.  Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[47]  D. W. Bolen,et al.  Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. , 1988, Biochemistry.

[48]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[49]  C. Pabo.  Molecular technology: Designing proteins and peptides , 1983, Nature.

[50]  H. Scheraga,et al.  Experimental and theoretical aspects of protein folding. , 1975, Advances in protein chemistry.

[51]  C. Levinthal.  Are there pathways for protein folding , 1968 .