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Automated scaffold selection for enzyme design

Title data

Malisi, Christoph ; Kohlbacher, Oliver ; Höcker, Birte:
Automated scaffold selection for enzyme design.
In: Proteins. Vol. 77 (October 2009) Issue 1 . - pp. 74-83.
ISSN 1097-0134
DOI: https://doi.org/10.1002/prot.22418

Abstract in another language

A major goal of computational protein design is the construction of novel functions on existing protein scaffolds. There the first question is which scaffold is suitable for a specific reaction. Given a set of catalytic residues and their spatial arrangement, one wants to identify a protein scaffold that can host this active site. Here, we present an algorithm called ScaffoldSelection that is able to rapidly search large sets of protein structures for potential attachment sites of an enzymatic motif. The method consists of two steps; it first identifies pairs of backbone positions in pocket-like regions. Then, it combines these to complete attachment sites using a graph theoretical approach. Identified matches are assessed for their ability to accommodate the substrate or transition state. A representative set of structures from the Protein Data Bank ( approximately 3500) was searched for backbone geometries that support the catalytic residues for 12 chemical reactions. Recapitulation of native active site geometries is used as a benchmark for the performance of the program. The native motif is identified in all 12 test cases, ranking it in the top percentile in 5 out of 12. The algorithm is fast and efficient, although dependent on the complexity of the motif. Comparisons to other methods show that ScaffoldSelection performs equally well in terms of accuracy and far better in terms of speed. Thus, ScaffoldSelection will aid future computational protein design experiments by preselecting protein scaffolds that are suitable for a specific reaction type and the introduction of a predefined amino acid motif.

Further data

Item Type: Article in a journal
Refereed: Yes
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry > Chair Biochemistry - Univ.-Prof. Dr. Birte Höcker
Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry
Result of work at the UBT: No
DDC Subjects: 500 Science > 540 Chemistry
Date Deposited: 01 Jun 2017 07:05
Last Modified: 01 Jun 2017 07:05
URI: https://eref.uni-bayreuth.de/id/eprint/37221