Design of Multi-Specificity in Protein Interfaces
نویسندگان
چکیده
منابع مشابه
Design of Multi-Specificity in Protein Interfaces
Interactions in protein networks may place constraints on protein interface sequences to maintain correct and avoid unwanted interactions. Here we describe a "multi-constraint" protein design protocol to predict sequences optimized for multiple criteria, such as maintaining sets of interactions, and apply it to characterize the mechanism and extent to which 20 multi-specific proteins are constr...
متن کاملSpecificity in Computational Protein Design*
A long-standing goal of computational protein design is to create proteins similar to those found in Nature. One motivation is to harness the exquisite functional capabilities of proteins for our own purposes. The extent of similarity between designed and natural proteins also reports on how faithfully our models represent the selective pressures that determine protein sequences. As the field o...
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BACKGROUND Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders. METHODOLOGY Here, we propose a new method for designing novel protein reagents that combines advantages of rede...
متن کاملPredicting affinity- and specificity-enhancing mutations at protein-protein interfaces.
Manipulations of PPIs (protein-protein interactions) are important for many biological applications such as synthetic biology and drug design. Combinatorial methods have been traditionally used for such manipulations, failing, however, to explain the effects achieved. We developed a computational method for prediction of changes in free energy of binding due to mutation that bring about deeper ...
متن کاملSpecificity versus stability in computational protein design.
Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and/or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more s...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2007
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.0030164