ArticleProceedings of the National Academy of Sciences of the United States of America2003
Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.ACS catalysis · 2017Article
- Article
- Computational protein engineering: bridging the gap between rational design and laboratory evolution.International journal of molecular sciences · 2012Review
- A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments.Proteins · 2012Article
- Optimization of combinatorial mutagenesis.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
- Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.Current drug targets · 2010Review
- Article
- A computational framework to empower probabilistic protein design.Bioinformatics (Oxford, England) · 2008Article
- Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- IPRO: an iterative computational protein library redesign and optimization procedure.Biophysical journal · 2006Article
- Gibbs sampling and helix-cap motifs.Nucleic acids research · 2005Article
- FamClash: a method for ranking the activity of engineered enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
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2 authors.
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Abstract
In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue-residue couplings consistent with a given protein structure. This information is subsequently used to classify protein hybrids with respect to their potential to be functional based on the presenceabsence and severity of clashing residue-residue interactions. First, atomistic representations of both the native and denatured states are used to calculate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer conformational energies. Next, this complete conformational energy table is coupled with a second-order mean-field description to elucidate the probabilities of all possible rotamer-rotamer combinations in a minimum Helmholtz free-energy ensemble. Computational results for the dihydrofolate reductase family reveal correlation in substitution patterns between not only contacting but also distal second-order structural elements. Residue-residue clashes in hybrid proteins are quantified by contrasting the ensemble probabilities of protein hybrids against the ones of the original parental sequences. Good agreement with experimental data is demonstrated by superimposing these clashes against the functional crossover profiles of bidirectional incremental truncation libraries for Escherichia coli and human glycinamide ribonucleotide transformylases.
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