CiteULike: msuarezdiez's computational_protein_design

De novo protein design using pairwise potentials and a genetic algorithm

DT Jones — 2008-04-29T09:22:40-00:00

Protein Sci, Vol. 3, No. 4. (1 April 1994), pp. 567-574.

The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors.

JS Marvin — 2008-04-25T09:19:27-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 94, No. 9. (29 April 1997), pp. 4366-4371.

Rational protein design is an emerging approach for testing general theories of structure and function. The ability to manipulate function rationally also offers the possibility of creating new proteins of biotechnological value. Here we use the design approach to test the current understanding of the structural principles of allosteric interactions in proteins and demonstrate how a simple allosteric system can form the basis for the construction of a generic biosensor molecular engineering system. We have identified regions in Escherichia coli maltose-binding protein that are predicted to be allosterically linked to its maltose-binding site. Environmentally sensitive fluorophores were covalently attached to unique thiols introduced by cysteine mutations at specific sites within these regions. The fluorescence of such conjugates changes cooperatively with respect to maltose binding, as predicted. Spatial separation of the binding site and reporter groups allows the intrinsic properties of each to be manipulated independently. Provided allosteric linkage is maintained, ligand binding can therefore be altered without affecting transduction of the binding event by fluorescence. To demonstrate applicability to biosensor technology, we have introduced a series of point mutations in the maltose-binding site that lower the affinity of the protein for its ligand. These mutant proteins have been combined in a composite biosensor capable of measuring substrate concentration within 5% accuracy over a concentration range spanning five orders of magnitude.

Protein structure prediction by global optimization of a potential energy function

Adam Liwo — 2008-04-24T16:37:18-00:00

Proceedings of the National Academy of Sciences, Vol. 96, No. 10. (11 May 1999), pp. 5482-5485.

10.1073/pnas.96.10.5482

Optimal Sequence Selection in Proteins of Known Structure by Simulated Evolution

HW Hellinga — 2008-04-22T11:48:36-00:00

Proceedings of the National Academy of Sciences, Vol. 91, No. 13. (21 June 1994), pp. 5803-5807.

10.1073/pnas.91.13.5803

Automatic sequence design of MHC Class-I binding peptides impairing CD8+ T cell recognition

Koji Ogata — 2008-04-22T10:50:59-00:00

J. Biol. Chem. (30 October 2002), M206853200.

An automatic protein design procedure is used to compute amino acid sequences of peptides likely to bind the HLA-A2 MHC class-I allele. The only information used by the procedure are a structural template, a rotamer library, and a well-established classical empirical force field. The calculations are performed on 6 different templates from x-ray structures of HLA-A0201-peptide complexes. Each template consists of the bound peptide backbone and the full atomic coordinates of the MHC protein. Sequences within 2 kcal/mol of the minimum energy sequence are computed for each template and the sequences from all he templates are combined and ranked by their energies. The 5 lowest energy peptide sequences and 5 other low energy sequences re-ranked on the basis of their similarity to peptides known to bind the same MHC allele, are chemically synthesised and tested for their ability to bind and form stable complexes with the HLA-A2 molecule. The most efficient binders are also tested for inhibition of the T-cell receptor (TCR) recognition of two known CD8+ T effectors. Results show that all 10 peptides bind the expected MHC protein. The 6 strongest binders also form stable HLA-A2-peptide complexes, albeit to varying degrees, and 3 peptides display significant inhibition of CD8+ T cell recognition. These results are rationalised in light of our knowledge of the 3D structures of the HLA-A2-peptide and HLA-A2-peptide-TCR complexes. 10.1074/jbc.M206853200

Engineered antibody Fc variants with enhanced effector function.

GA Lazar — 2006-05-01T16:44:11-00:00

Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4005-4010.

Antibody-dependent cell-mediated cytotoxicity, a key effector function for the clinical efficacy of monoclonal antibodies, is mediated primarily through a set of closely related Fcgamma receptors with both activating and inhibitory activities. By using computational design algorithms and high-throughput screening, we have engineered a series of Fc variants with optimized Fcgamma receptor affinity and specificity. The designed variants display >2 orders of magnitude enhancement of in vitro effector function, enable efficacy against cells expressing low levels of target antigen, and result in increased cytotoxicity in an in vivo preclinical model. Our engineered Fc regions offer a means for improving the next generation of therapeutic antibodies and have the potential to broaden the diversity of antigens that can be targeted for antibody-based tumor therapy.

De Novo Computational Design of Retro-Aldol Enzymes

Lin Jiang — 2008-03-07T02:58:37-00:00

Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model. 10.1126/science.1152692